MORALES-BRIONES ET AL. 1

SUPPLEMENTARY METHODS

Library preparation

Library preparation was carried out using either poly-A enrichment of ribosomal RNA depletion.

For Tidestromia oblongifolia, tissue collection, RNA isolation, library preparation was carried out using the KAPA Stranded mRNA-Seq Kits (KAPA Biosystems, Wilmington, Massachusetts,

USA). The library was multiplexed with 10 other samples from a different project on an Illumina

HiSeq2500 platform with V4 chemistry at the University of Michigan Sequencing Core. For the remaining 16 samples total RNA was isolated from c. 70-125 mg leaf tissue collected in liquid nitrogen using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s protocol (June

2012). A DNase digestion step was included with the RNase-Free DNase Set (Qiagen). Quality and quantity of RNA were checked using the 2100 Bioanalyzer (Agilent Technologies). Library preparation was carried out using the TruSeq® Stranded Total RNA Library Prep Plant with

RiboZero probes (96 Samples. Illumina, #20020611; Schuierer et al. 2017). Indexed libraries were normalized, pooled and size selected to 320bp +/- 5% using the Pippin Prep HT instrument to generate libraries with mean inserts of 200 bp, and sequenced on the Illumina HiSeq2500 platform with V4 chemistry at the University of Minnesota Genomics Center. Reads from all 17 libraries were paired-end 125 bp.

MORALES-BRIONES ET AL. 2

Transcriptome data processing and assembly

Scripts and instructions for read processing, assembly, translation, and homology and orthology search can be found at https://bitbucket.org/yanglab/phylogenomic_dataset_construction/ as part of an updated ‘phylogenomic dataset construction’ pipeline (Yang and Smith 2014).

We processed raw reads for all 88 transcriptome datasets (except Bienertia sinuspersici) used in this study (Table S1). Sequencing errors in raw reads were corrected with Rcorrector

(Song and Florea 2015) and reads flagged as uncorrectable were removed. Sequencing adapters and low-quality bases were removed with Trimmomatic v0.36 (ILLUMINACLIP:

TruSeq_ADAPTER: 2:30:10 SLIDINGWINDOW: 4:5 LEADING: 5 TRAILING: 5 MINLEN:

25; Bolger et al. 2014). Additionally, chloroplast and mitochondrial reads were filtered with

Bowtie2 v 2.3.2 (Langmead and Salzberg 2012) using publicly available Caryophyllales organelle genomes from the Organelle Genome Resources database (RefSeq; [Pruitt et al. 2007]; last accessed on October 17, 2018) as references. Read quality was assessed with FastQC v

0.11.7 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Overrepresented sequences detected with FastQC were discarded. De novo assembly was carried out with Trinity v 2.5.1

(Grabherr et al. 2011) with default settings, but without in silico normalization. Assembly quality was assessed with Transrate v 1.0.3 (Smith-Unna et al. 2016). Low quality and poorly supported transcripts were removed using individual cut-off values for three contig score components of

Transrate: 1) proportion of nucleotides in a contig that agrees in identity with the aligned read, s(Cnuc) ≤ 0.25; 2) proportion of nucleotides in a contig that have one or more mapped reads, s(Ccov) ≤0.25; and 3) proportion of reads that map to the contig in correct orientation, s(Cord) ≤

0.5. Furthermore, chimeric transcripts (trans-self and trans-multi-gene) were removed following the approach described in Yang and Smith (2013) using Beta vulgaris as the reference proteome, MORALES-BRIONES ET AL. 3 and percentage similarity and length cutoffs of 30 and 100, respectively. In order to remove isoforms and assembly artifacts, filtered reads were remapped to filtered transcripts with Salmon v 0.9.1 (Patro et al. 2017) and putative genes were clustered with Corset v 1.07 (Davidson and

Oshlack 2014) using default settings, except that we used a minimum of five reads as threshold to remove transcripts with low coverage (-m 5). Only the longest transcript of each putative gene inferred by Corset was retained (Chen et al. 2019). Filtered transcripts were translated with

TransDecoder v 5.0.2 (Haas et al. 2013) with default settings and the proteome of Beta vulgaris and Arabidopsis thaliana to identify open reading frames. Finally, coding sequences (CDS) from translated amino acids were further reduced with CD-HIT v 4.7 (-c 0.99; [Fu et al. 2012]) to remove near-identical sequences.

Homology and orthology inference of nuclear genes

Initial homology inference was carried out following Yang and Smith (2014) with some modifications. First, an all-by-all BLASTN search was performed on CDS using an E value cutoff of 10 and max_target_seqs set to 100. Raw BLAST output was filtered with a hit fraction of 0.4. Then putative homologs groups were clustered using MCL v 14-137 (van Dongen 2000) with a minimum minus log-transformed E value cutoff of 5 and an inflation value of 1.4. Finally, only clusters with a minimum of 25 taxa were retained. Individual clusters were aligned using

MAFFT v 7.307 (Katoh and Standley 2013) with settings ‘–genafpair –maxiterate 1000’.

Aligned columns with more than 90% missing data were removed using Phyx (Brown et al.

2017). Homolog trees were built using RAxML v 8.2.11 (Stamatakis 2014) with a GTRCAT model and clade support assessed with 200 rapid bootstrap (BS) replicates. Spurious or outlier long tips were detected and removed with TreeShrink v 1.0.0. by maximally reducing the tree MORALES-BRIONES ET AL. 4 diameter (Mai and Mirarab 2018). Monophyletic and paraphyletic tips that belonged to the same taxon were removed keeping the tip with the highest number of characters in the trimmed alignment. After visual inspection of ca. 50 homolog trees, we determined that internal branches longer than 0.25 were likely representing deep paralogs. These branches were cut apart, keeping resulting subclades with a minimum of 25 taxa. Homolog tree inference, tip and outlier removal, and deep paralog cutting was carried out for a second time using the same settings to obtain final homologs. Orthology inference was carried out following the ‘monophyletic outgroup’ approach from Yang and Smith (2014), keeping only ortholog groups with at least 25 ingroup taxa. The

‘monophyletic outgroup’ approach filters for clusters that have outgroup taxa being monophyletic and single-copy, and therefore filters for single- and low-copy genes. It then roots the gene tree by the outgroups, traverses the rooted tree from root to tip, and removes the side with less taxa when gene duplication is detected.

Synteny analyses

To visualize any genomic patterns of the phylogenetic history of Beta vulgaris regarding its relationship with Amaranthaceae s.s. and Chenopodiaceae, we first identified syntenic regions between the genomes of Beta vulgaris and the outgroup Mesembryanthemum crystallinum using the SynNet pipeline (https://github.com/zhaotao1987/SynNet-Pipeline; Zhao and Schranz 2019).

We used DIAMOND v.0.9.24.125 (Buchfink et al. 2015) to perform all-by-all inter- and intra- pairwise protein searches with default parameters, and MCScanX (Wang et al. 2012) for pairwise synteny block detection with default parameters, except match score (-k) that was set to five. Then, we plot the nine chromosomes of Beta vulgaris by assigning each of the 8,258 orthologs of the quartet composed of Mesembryanthemum crystallinum (outgroup), Amaranthus MORALES-BRIONES ET AL. 5 hypochondriacus, Beta vulgaris, and Chenopodium quinoa (BC1A) to synteny blocks and to one of the three possible quartet topologies based on best likelihood score.

Assessment of substitutional saturation, codon usage bias, compositional heterogeneity, and

model of sequence evolution misspecification

We refiltered the final 105-taxon ortholog alignments to again include genes that have the same

11 taxa (referred herein as 11-taxon(tree) dataset used for the species network analyses. We realigned individual genes using MACSE v.2.03 (Ranwez et al. 2018) to account for codon structure and frameshifts. Codons with frameshifts were replaced with gaps, and ambiguous alignment sites were removed using GBLOCKS v0.9b (Castresana 2000) while accounting for codon alignment (-t=c -b1=6 -b2=6 -b3=2 -b4=2 -b5=h). After realignment and removal of ambiguous sites, we kept genes with a minimum of 300 aligned base pairs. To detect potential saturation, we plotted the uncorrected genetic distances against the inferred distances as described in Philippe and Forterre (1999). The level of saturation was determined by the slope of the linear regression between the two distances where a shallow slope (i.e < 1) indicates saturation. We estimated the level of saturation by concatenating all genes and dividing the first and second codon positions from the third codon positions. We calculated uncorrected, and inferred distances with the TN93 substitution model using APE v5.3 (Paradis and Schliep 2019) in R. To determine the effect of saturation in the phylogenetic inferences we estimated individual gene trees using three partition schemes. We inferred ML trees with an unpartitioned alignment, a partition by first and second codon positions, and the third codon positions, and by removing all third codon positions. All tree searches were carried out in RAxML with a GTRGAMMA model and 200 bootstrap replicates. A species tree for each of the three data schemes was MORALES-BRIONES ET AL. 6 estimated with ASTRAL-III v5.6.3 (Zhang et al. 2018) and gene tree discordance was examined with PhyParts (Smith et al. 2015).

Codon usage bias was evaluated using a correspondence analysis of the Relative

Synonymous Codon Usage (RSCU), which is defined as the number of times a particular codon is observed relative to the number of times that the codon would be observed in the absence of any codon usage bias (Sharp and Li 1986). RSCU for each codon in the 11-taxon concatenated alignment was estimated with CodonW v.1.4.4 (Peden 1999). Correspondence analysis was carried out using FactoMineR v1.4.1(Lê et al. 2008) in R (R Core Team 2019). . To determine the effect of codon usage bias in the phylogenetic inferences we estimated individual gene trees using codon-degenerated alignments. Alignments were recoded to eliminate signals associated with synonymous substitutions by degenerating the first and third codon positions using ambiguity coding using DEGEN v1.4 (Regier et al. 2010; Zwick et al. 2012). Gene tree inference and discordance analyses were carried out on the same three data schemes as previously described.

To examine the presence of among-lineage compositional heterogeneity, individual genes were evaluated using the compositional homogeneity test that uses a null distribution from simulations as proposed by Foster (2004). We performed the compositional homogeneity test by optimizing individual gene trees with a GTRGAMMA model and 1,000 simulations in P4

(Foster 2004). To assess if compositional heterogeneity had an effect in species tree inference and gene tree discordance, gene trees that showed the signal of compositional heterogeneity were removed from saturation and codon usage analyses and the species tree and discordance analyses were rerun. MORALES-BRIONES ET AL. 7

To explore the effect of sequence evolution model misspecification, we reanalyzed the datasets from the saturation and codon usage analyses using inferred gene trees that accounted for model selection. We performed extended model selection followed by ML gene tree inference and 1,000 ultrafast bootstrap replicates for branch support in IQ-Tree v.1.6.1 (Nguyen et al. 2015). Species tree inference, conflict analysis and removal of genes with compositional heterogeneity were carried out as previously described.

Finally, we also used amino acid alignments from MACSE to account for substitutional saturation. Amino acid positions with frameshifts were replaced with gaps, and ambiguous alignment sites were removed with Phyx requiring a minimal occupancy of 30%. We inferred individual gene trees with IQ-tree to account for a model of sequence evolution and carried out species tree inference, conflict analysis, and removal of genes with compositional heterogeneity as described for the nucleotide alignments.

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92 ingroup species (88 transcriptomes, 4 genomes) 13 outgroups (10 transcriptomes, 3 genomes)

Choloroplast assembly and contig lltering

11-taxon 103-taxon Read processing, de novo 76 genes and 76 genes and assembly, transcript ltering, ≥ 6 taxa ≥ 51 taxa translation, and homolgy and orthology inferences

Concatenated best Model of sequence Concatenated best model partion & evolution & gene model partion & tree inference with tree inference with tree inference with IQ-tree IQ-tree IQ-tree

PhyParts Quartet concordance sampling 13,024 orthologs analyses ≥ 25 spp.

Assesment of recombination 12,932 orthologs

41-taxon 11-taxon(net) 4-taxon (10 quartets) 105-taxon 11-taxon(tree) 1,242 genes with no 4,138 genes with no Between 7,756 and 936 genes, ≥ 99 spp., and 5,936 genes with no missing taxa and missing taxa and ≥ 8,793 genes with ≥1,000 bp. missing taxa and ≥ 1,000 bp. 1,000 bp. ≥300 bp ≥300 bp.

Gene tree ASTRAL Concatenated Gene tree ASTRAL Gene tree Concatenated Gene tree Assesment of Assesment of Assesment of inference species tree matrix - RAxML inference species tree inference matrix - RAxML inference substitutional codon usage compositional saturation bias heterogeneity PhyParts Cloudogram PhyParts Quartet concordance ASTRAL PhyParts Removal of ASTRAL PhyloNet species PhyloNet species AU topology ABBA/BABA Standard Degenerated concordance sampling analyses species tree concordance compositional species tree networks networks test test bases bases analyses analyses heterogenous genes

No Codon 1 & 2 Amino partition partition codon Acid

Model of sequence RAxML gene tree evolution & gene inference with tree inference with GTRGAMMA IQ-tree

ASTRAL PhyParts ASTRAL species tree concordance polytomy test analyses FIGURE S1. Overview of all datasets (red boxes) and analyses (blue boxes and arrows) in this study. 677/31 Suaeda divaricata 437/286 Discordant 0.88 Suaeda fruticosa 304/388 0.63 (main alternative) Suaeda ifniensis 760/72 0.52 Suaeda aralocaspica Discordant 901/15 0.82 Suaeda vera (remaining alternatives) Concordant 0.92 887/32 Suaeda glauca 0.87 804/84 Suaeda maritima 694/173 931/0 0.90 Suaeda salsa 0.82 1.00 Suaeda linearis Bienertia sinuspersici 899/13 Salicornia pacifica Uninformative 911/23 669/205 0.94 Salicornia europaea 0.88 859/43 0.83 Tecticornia pergranulata 274/509 0.84 Arthrocaulon macrostachyum 723/113 0.57 Kalidium cuspidatum Chenopods II 921/11 0.79 Halostachys caspica 0.92 906/15 Allenrolfea sp. 0.93 Heterostachys sp. 916/14 196/505 Halogeton glomeratus 0.91 453/281 0.30 Salsola oppositifolia 319/409 0.47 102/514 Haloxylon ammodendron Hammada scoparia 755/57 0.48 0.21 Salsola soda 678/165 0.84 Anabasis articulata 756/117 0.81 Kali collina 822/60 0.84 Salsola webbii 0.87 909/15 Caroxylon vermiculatum 0.90 872/11 Bassia scoparia 0.94 Eokochia saxicola 886/15 Atriplex lentiformis 529/286 0.95 Atriplex sp. 926/7 0.76 Atriplex rosea 0.97 432/358 Atriplex hortensis 0.72 Atriplex prostrata 901/22 231/401 780/80 Grayia brandegeei 0.92 518/253 0.42 0.86 Grayia spinosa 401/343 0.71 Extriplex californica 919/3 0.69 Stutzia covillei 927/7 0.98 Proatriplex pleiantha 0.94 659/183 Chenopodium quinoa 854/63 0.81 Chenopodium suecicum 823/52 97/7 0.86 Chenopodium amaranticolor 0.87 867/37 0.93 Chenopodium pallidicaule Chenopods I 0.89 Chenopodium vulvaria 480/255 Oxybasis rubra 0.65 548/36 Spinacia oleracea 126/453 912/0 0.88 Spinacia turkestanica 919/15 0.28 592/158 1.00 Spinacia tetrandra 0.94 0.72 Blitum bonus−henricus 902/20 Dysphania schraderiana 870/24 891/17 0.95 Dysphania ambrosioides 247/455 0.89 0.93 Suckleya suckleyana 0.49 Krascheninnikovia lanata 897/11 Agriophyllum squarrosum 116/435 0.94 Corispermum hyssopifolium 0.29 480/312 Beta vulgaris 358/418 0.70 Beta vulgaris 905/1 0.58 Beta maritima 896/20 0.99 Beta macrocarpa Betoideae 0.88 514/298 Patellifolia patellaris 0.76 Hablitzia tamnoides 917/8 Polycnemum majus Polycnemoideae 0.95 Nitrophila occidentalis 687/146 Gomphrena celosoides 753/109 0.87 Blutaparon vermiculare 890/17 0.85 Gossypianthus lanuginosus 896/11 0.94 Guilleminea densa 0.91 790/68 Froelichia latifolia 328/431 Pfaffia tuberosa 922/8 0.77 695/110 0.63 Gomphrena elegans 0.94 296/435 0.79 Quaternella ephedroides 0.36 582/214 Alternanthera brasiliana 869/10 0.86 Alternanthera philoxeroides 565/257 886/21 0.96 Alternanthera sessilis 0.50 0.91 887/13 Alternanthera caracasana 0.96 Alternanthera tenella 354/513 903/4 Tidestromia oblongifolia 0.34 0.98 Tidestromia lanuginosa Amaranthaceae s.s. 871/7 802/14 Achyranthes bidentata 0.96 0.94 Nelsia quadrangula 616/80 735/44 Aerva javanica 0.83 362/378 0.88 Aerva lanata 0.46 746/48 Iresine rhizomatosa 775/54 0.86 Iresine arbuscula 0.85 759/69 Amaranthus retroflexus 661/159 0.86 Amaranthus hyponchondriacus 288/507 0.78 Amaranthus palmeri 929/0 0.57 Amaranthus tuberculatus 1.00 872/19 Amaranthus tricolor 578/72 887/27 0.94 Amaranthus cruentus 0.79 0.93 599/211 Deeringia amaranthoides 0.82 Hermbstaedtia glauca 903/4 Achatocarpus gracilis 0.97 Phaulothamnus spinescens 733/51 Spergularia media 157/262 606/133 0.90 Dianthus caryophyllus 0.40 519/181 0.80 Illecebrum verticillatum 826/14 0.80 Herniaria latifolia 0.93 Corrigiola litoralis 835/2 Mesembryanthemum crystallinum 411/173 0.98 Delosperma echinatum 212/253 0.73 Commicarpus scandens 0.46 Mollugo pentaphylla Microtea debilis Fagopyrum tataricum

FIGURE S2. Maximum likelihood cladogram of Amaranthaceae s.l. inferred from RAxML analysis of the concatenated 936-nuclear gene supermatrix. Numbers above branches indicate the number of gene trees concordant/conflicting with that node in the species tree. Numbers below the branches are the Internode Certainty All (ICA) score. Pie charts on nodes present the proportion of gene trees that support that clade (blue), the proportion that support the main alternative bifurcation (green), the proportion that support the remaining alternatives (red), and the proportion (conflict or support) that have < 50% bootstrap support (gray). 1/–/1 Suaeda divaricata 1/–/1 Suaeda fruticosa 0.81/0/1 Suaeda ifniensis 1/–/1 Suaeda aralocaspica 1/–/1 Suaeda vera 1/–/1 Suaeda glauca 1/–/1 Suaeda maritima 0.76/0/1 1/–/1 Suaeda salsa Suaeda linearis Bienertia sinuspersici 1/–/1 Salicornia pacifica 1/–/1 0.81/0/1 Salicornia europaea 1/–/1 Tecticornia pergranulata −0.42/0.55/1 Arthrocaulon macrostachyum 1/–/1 Kalidium cuspidatum Chenopods II 1/–/1 Halostachys caspica 1/–/1 Allenrolfea sp. Heterostachys sp. 1/–/1 0.27/0.14/0.99 Halogeton glomeratus 1/–/1 Salsola oppositifolia 0.69/0.75/0.98 Haloxylon ammodendron Hammada scoparia 1/–/1 0.2/0.27/0.96 1/–/1 Salsola soda 1/–/1 Anabasis articulata 1/–/1 Kali collina Salsola webbii Caroxylon vermiculatum 1/–/1 1/–/1 Bassia scoparia Eokochia saxicola 1/–/1 Atriplex lentiformis 1/–/1 Atriplex sp. 1/–/1 Atriplex rosea 0.81/0/1 Atriplex hortensis Atriplex prostrata 0.25/0.19/0.99 1/–/1 1/–/1 Grayia brandegeei 1/–/1 Grayia spinosa 0.81/0/1 Extriplex californica Stutzia covillei 1/–/1 1/–/1 Proatriplex pleiantha 0.92/0/1 Chenopodium quinoa −0.0026/0/1 Chenopodium suecicum 1/–/1 1/–/1 Chenopodium amaranticolor 1/–/1 Chenopodium pallidicaule Chenopods I Chenopodium vulvaria 1/–/1 Oxybasis rubra 1/–/1 Spinacia oleracea 0.31/0.57/1 1/–/1 Spinacia turkestanica 1/–/1 1/–/1 Spinacia tetrandra Blitum bonus−henricus 1/–/1 Dysphania schraderiana 1/–/1 Dysphania ambrosioides −0.14/0.33/0.98 Suckleya suckleyana 1/–/1 Krascheninnikovia lanata 0.3/0.81/0.99 1/–/1 Agriophyllum squarrosum Corispermum hyssopifolium 1/–/1 Beta vulgaris 1/–/1 Beta vulgaris 1/–/1 Beta maritima 1/–/1 Beta macrocarpa Betoideae 1/–/1 Patellifolia patellaris Hablitzia tamnoides 1/–/1 Polycnemum majus Nitrophila occidentalis Polycnemoideae 1/–/1 Gomphrena celosoides 1/–/1 Blutaparon vermiculare 1/–/1 Gossypianthus lanuginosus 1/–/1 Guilleminea densa 1/–/1 Froelichia latifolia 1/–/1 0.69/1/0.99 Pfaffia tuberosa 1/–/1 Gomphrena elegans 0.64/0.36/1 Quaternella ephedroides 1/–/1 Alternanthera brasiliana 1/–/1 Alternanthera philoxeroides 1/–/1 1/–/1 Alternanthera sessilis 1/–/1 Alternanthera caracasana 0.76/0/1 Alternanthera tenella 1/–/1 Tidestromia oblongifolia Tidestromia lanuginosa Amaranthaceae s.s. 1/–/1 1/–/1 Achyranthes bidentata Nelsia quadrangula 0.92/0/1 1/–/1 Aerva javanica 1/–/1 Aerva lanata Iresine rhizomatosa 0.92/0/1 1/–/1 Iresine arbuscula 1/–/1 Amaranthus retroflexus 1/–/1 Amaranthus hyponchondriacus −0.52/0.025/0.99 Amaranthus palmeri 1/–/1 Amaranthus tuberculatus 1/–/1 1/–/1 1/–/1 Amaranthus tricolor Amaranthus cruentus 1/–/1 Deeringia amaranthoides Hermbstaedtia glauca 1/–/1 Achatocarpus gracilis Phaulothamnus spinescens 1/–/1 Spergularia media 0.76/0/1 1/–/1 Dianthus caryophyllus 1/–/1 Illecebrum verticillatum 1/–/1 Herniaria latifolia Corrigiola litoralis 1/–/1 Mesembryanthemum crystallinum 1/–/1 Delosperma echinatum 0.76/0/0.99 Commicarpus scandens Mollugo pentaphylla Microtea debilis Fagopyrum tataricum

FIGURE S3. Maximum likelihood cladogram of Amaranthaceae s.l. inferred from RAxML analysis of the concatenated 936-nuclear gene supermatrix. Numbers above branches indicate the

Quartet sampling internal node score. Quartet concordance/Quartet differential/ Quartet informativeness. Scores in blue indicate strong support for the species tree topology, while red scores indicate strong support for alternative topologies.

Gomphrena celosoides Blutaparon vermiculare Gossypianthus lanuginosus Discordant Guilleminea densa (main alternative) Froelichia latifolia 79 Quaternella ephedroides Gomphrena elegans Discordant Pfaffia tuberosa (remaining Concordant Alternanthera philoxeroides Gomphrenoids Alternanthera brasiliana alternatives) Alternanthera sessilis 99 Alternanthera tenella Alternanthera caracasana Uninformative Tidestromia oblongifolia Tidestromia lanuginosa Amaranthaceae s.s. Iresine arbuscula Iresine rhizomatosa Nelsia quadrangula Achyranthes bidentata Achyranthoids Aerva lanata Aerva javanica Aervoids Amaranthus tuberculatus Amaranthus palmeri Amaranthus retroflexus Amaranthus hypochondriacus Amaranthoids Amaranthus cruentus Amaranthus tricolor Hermbstaedtia glauca Deeringia amaranthoides Celosioids Polycnemum majus Nitrophila occidentalis Polycnemoideae Atriplex lentiformis Atriplex sp. Atriplex rosea Atriplex hortensis Atriplex prostrata Grayia spinosa Grayia brandegeei Extriplex californica Stutzia covillei 73 Proatriplex pleiantha Chenopodium suecicum Chenopodium amaranticolor Chenopodioideae Chenopodium pallidicaule Chenopods I Chenopodium quinoa Chenopodium vulvaria Oxybasis rubra Spinacia tetrandra Spinacia oleracea 95 Blitum bonus−henricus Suckleya suckleyana Dysphania ambrosioides Krascheninnikovia lanata Corispermum hyssopifolium Agriophyllum squarrosum Corispermoideae 90 Beta vulgaris 86 Beta vulgaris Beta maritima Beta macrocarpa Betoideae Amaranthaceae s.l. Patellifolia patellaris Hablitzia tamnoides Suaeda fruticosa Suaeda divaricata Suaeda ifniensis Suaeda vera Suaeda aralocaspica Suaedoideae Suaeda glauca 98 Suaeda salsa Suaeda linearis Suaeda maritima Bienertia sinuspersici Salicornia europaea Salicornia pacifica Tecticornia pergranulata Arthrocaulon macrostachyum Kalidium cuspidatum Salicornioideae Chenopods II Halostachys caspica Allenrolfea sp. Heterostachys sp. 95 Salsola oppositifolia 89 Haloxylon ammodendron Halogeton glomeratus Hammada scoparia Salsola soda Salsoloidae Anabasis articulata Salsola webbii Kali collina Caroxylon vermiculatum Bassia scoparia Eokochia saxicola Camphorosmoideae Achatocarpus gracilis Phaulothamnus spinescens 91 Spergularia media substitution per site 98 Dianthus caryophyllus 0.01 Illecebrum verticillatum Herniaria latifolia Corrigiola litoralis Delosperma echinatum Mesembryanthemum crystallinum Commicarpus scandens Mollugo pentaphylla Microtea debilis Fagopyrum tataricum

FIGURE S4. Maximum likelihood phylogeny of Amaranthaceae s.l. inferred from IQ-tree analysis of concatenated 76-plastid gene supermatrix. All nodes have full support (Bootstrap

= 100) unless noted next to nodes. Pie charts present the proportion of gene trees that support that clade (blue), the proportion that support the main alternative bifurcation (green), the proportion that support the remaining alternatives (red), and the proportion (conflict or support) that have < 50% bootstrap support (gray). Only pie charts for major clades are shown (see Fig.

S5 for all node pie charts). Branch lengths are in number of substitutions per site.

13/16 Gomphrena celosoides 41/12 Discordant 0.22 Blutaparon vermiculare 36/21 0.48 Gossypianthus lanuginosus (main alternative) 43/18 0.35 Guilleminea densa Discordant 0.36 Froelichia latifolia (remaining alternatives) Concordant 37/22 0.26 14/29 Quaternella ephedroides 37/17 0.19 Gomphrena elegans 0.35 Pfaffia tuberosa 16/42 42/3 Alternanthera philoxeroides 0.07 46/6 0.74 Alternanthera brasiliana 47/10 0.67 Alternanthera sessilis Uninformative 0.58 42/3 Alternanthera tenella 19/38 16/38 0.77 Alternanthera caracasana 0.08 0.12 59/4 Tidestromia oblongifolia 29/33 0.77 Tidestromia lanuginosa Amaranthaceae s.s. 0.13 28/19 Iresine arbuscula 0.27 Iresine rhizomatosa 53/11 42/6 Nelsia quadrangula 0.43 0.67 Achyranthes bidentata 32/15 Aerva lanata 0.36 Aerva javanica 41/25 14/11 Amaranthus tuberculatus 0.21 20/22 0.21 Amaranthus palmeri 0.17 10/14 Amaranthus retroflexus 62/6 0.14 Amaranthus hypochondriacus 0.62 15/47 36/24 36/2 Amaranthus cruentus 0.07 0.30 0.74 Amaranthus tricolor 18/37 Hermbstaedtia glauca 0.22 Deeringia amaranthoides 45/7 Polycnemum majus 0.66 Nitrophila occidentalis Polycnemoideae 12/7 Atriplex lentiformis 24/24 0.29 Atriplex sp. 51/8 0.28 Atriplex rosea 0.56 40/9 Atriplex hortensis 0.53 Atriplex prostrata 47/24 21/20 Grayia spinosa 0.35 22/32 0.23 Grayia brandegeei 39/23 0.18 Extriplex californica 56/13 0.36 Stutzia covillei 64/9 4/58 0.48 Proatriplex pleiantha −0.03 0.56 26/6 Chenopodium suecicum 26/30 0.51 Chenopodium amaranticolor 39/27 0.24 23/20 Chenopodium pallidicaule Chenopods I 0.27 48/14 0.55 0.27 Chenopodium quinoa Chenopodium vulvaria 37/34 Oxybasis rubra 0.12 15/1 Spinacia tetrandra 48/9 0.66 Spinacia oleracea 18/29 15/48 0.53 Blitum bonus−henricus 0.14 0.09 43/15 Suckleya suckleyana 34/34 0.42 Dysphania ambrosioides 0.14 Krascheninnikovia lanata 50/8 Corispermum hyssopifolium Agriophyllum squarrosum 20/47 0.64 Beta vulgaris 0.06 16/15 24/10 0.14 Beta vulgaris 35/3 0.31 Beta maritima 37/29 0.71 Beta macrocarpa Betoideae 0.23 51/18 31/23 Patellifolia patellaris 0.29 0.33 Hablitzia tamnoides 31/4 Suaeda fruticosa 34/21 0.68 Suaeda divaricata 38/30 0.34 Suaeda ifniensis 47/21 0.22 25/31 Suaeda vera 0.30 0.16 Suaeda aralocaspica 45/28 Suaeda glauca 0.27 32/26 Suaeda salsa 39/32 44/2 0.31 Suaeda linearis 0.21 0.81 Suaeda maritima Bienertia sinuspersici 43/7 Salicornia europaea 50/23 33/25 0.59 Salicornia pacifica 0.27 37/22 0.33 Tecticornia pergranulata 40/24 0.32 Arthrocaulon macrostachyum 45/25 0.33 40/15 Kalidium cuspidatum 51/14 Chenopods II 0.24 0.46 Halostachys caspica 0.53 40/8 Allenrolfea sp. 0.55 Heterostachys sp. 42/28 7/11 Salsola oppositifolia 0.19 20/29 0.10 Haloxylon ammodendron 26/18 0.14 Halogeton glomeratus 12/20 0.25 Hammada scoparia 43/17 0.24 Salsola soda 15/19 0.35 Anabasis articulata 31/38 0.34 35/33 Salsola webbii 0.15 0.27 Kali collina 53/15 13/24 Caroxylon vermiculatum 0.44 0.13 29/1 Bassia scoparia 0.70 Eokochia saxicola 58/0 Achatocarpus gracilis 1.00 Phaulothamnus spinescens 9/47 41/10 Spergularia media −0.09 18/37 0.45 Dianthus caryophyllus 29/34 0.15 Illecebrum verticillatum 41/16 0.18 Herniaria latifolia 0.34 Corrigiola litoralis 39/5 Delosperma echinatum 22/21 0.55 Mesembryanthemum crystallinum 13/41 0.25 Commicarpus scandens 0.09 Mollugo pentaphylla Microtea debilis Fagopyrum tataricum

FIGURE S5. Maximum likelihood cladogram of Amaranthaceae s.l. inferred from IQ-tree

analysis of concatenated 76-plastid gene supermatrix. Numbers above branches indicate the

number of gene trees concordant/conflicting with that node in the species tree. Numbers below

the branches are the Internode Certainty All (ICA) score. Pie charts on nodes present the

proportion of gene trees that support that clade (blue), the proportion that support the main

alternative bifurcation (green), the proportion that support the remaining alternatives (red), and

the proportion (conflict or support) that have < 50% bootstrap support (gray). 1/NA/0.82 Gomphrena celosoides 1/–/1 Blutaparon vermiculare 1/–/1 Gossypianthus lanuginosus 1/–/1 Guilleminea densa 1/–/1 Froelichia latifolia −0.19/0.25/0.61 Quaternella ephedroides 1/–/1 Gomphrena elegans Pfaffia tuberosa 0.78/0.11/0.89 1/–/1 Alternanthera philoxeroides 1/–/1 Alternanthera brasiliana 1/–/1 Alternanthera sessilis 1/–/1 Alternanthera tenella 0.48/0.72/0.76 0.19/0.92/0.71 Alternanthera caracasana 1/–/1 Tidestromia oblongifolia 0.9/0.3/0.92 Tidestromia lanuginosa Amaranthaceae s.s. 0.99/0/1 Iresine arbuscula Iresine rhizomatosa 1/–/1 1/–/1 Nelsia quadrangula Achyranthes bidentata 1/–/1 Aerva lanata Aerva javanica 1/–/1 1/NA/0.97 Amaranthus tuberculatus 0.94/1/0.95 Amaranthus palmeri 1/–/1 Amaranthus retroflexus 1/–/1 Amaranthus hypochondriacus 0.41/0.21/0.78 1/–/1 1/–/1 Amaranthus cruentus Amaranthus tricolor 0.65/0.069/0.84 Hermbstaedtia glauca Deeringia amaranthoides 1/–/1 Polycnemum majus Nitrophila occidentalis Polycnemoideae 1/–/1 Atriplex lentiformis 0.92/0/0.96 Atriplex sp. 1/–/1 Atriplex rosea 1/–/1 Atriplex hortensis Atriplex prostrata 1/–/1 1/NA/0.93 Grayia spinosa 0.95/0/0.85 Grayia brandegeei 1/–/1 Extriplex californica 1/–/1 Stutzia covillei 1/–/1 −0.29/0.42/0.75 Proatriplex pleiantha 1/–/1 Chenopodium suecicum 1/–/1 Chenopodium amaranticolor 1/–/1 Chenopods I 1/–/1 1/–/1 Chenopodium pallidicaule Chenopodium quinoa Chenopodium vulvaria 0.91/0.5/0.86 Oxybasis rubra 1/–/1 Spinacia tetrandra 1/–/1 Spinacia oleracea 0.96/0/0.98 0.038/0.95/0.6 Blitum bonus−henricus 1/–/1 Suckleya suckleyana 0.99/0/1 Dysphania ambrosioides Krascheninnikovia lanata 1/–/1 Corispermum hyssopifolium Agriophyllum squarrosum 0.84/0.88/0.94 0.39/0/0.47 Beta vulgaris 0.7/1/0.63 Beta vulgaris 1/–/1 Beta maritima 1/–/1 Beta macrocarpa Betoideae 1/–/1 1/–/1 Patellifolia patellaris Hablitzia tamnoides 1/–/1 Suaeda fruticosa 1/–/1 Suaeda divaricata 1/NA/0.99 Suaeda ifniensis 1/–/1 0.41/0.3/0.76 Suaeda vera Suaeda aralocaspica 1/–/1 Suaeda glauca 0.24/0/0.41 Suaeda salsa 1/–/1 1/–/1 Suaeda linearis Suaeda maritima Bienertia sinuspersici 1/–/1 Salicornia europaea 1/–/1 1/–/1 Salicornia pacifica 1/–/1 Tecticornia pergranulata 1/–/1 Arthrocaulon macrostachyum 1/–/1 1/–/1 Kalidium cuspidatum 1/–/1 Chenopods II Halostachys caspica 1/–/1 Allenrolfea sp. Heterostachys sp. 1/–/1 0.84/1/0.58 Salsola oppositifolia 0.38/0.76/0.47 Haloxylon ammodendron 1/NA/0.97 Halogeton glomeratus 0.81/0/0.72 Hammada scoparia 1/–/1 Salsola soda 1/NA/0.99 Anabasis articulata 0.95/0/0.99 0.93/0.91/0.91 Salsola webbii Kali collina 1/–/1 1/NA/0.95 Caroxylon vermiculatum 1/–/1 Bassia scoparia Eokochia saxicola 1/–/1 Achatocarpus gracilis Phaulothamnus spinescens 0.78/0.82/0.83 1/–/1 Spergularia media 0.89/1/0.92 Dianthus caryophyllus 0.97/0/0.99 Illecebrum verticillatum 1/–/1 Herniaria latifolia Corrigiola litoralis 1/–/1 Delosperma echinatum 1/–/1 Mesembryanthemum crystallinum 0.37/0.028/0.63 Commicarpus scandens Mollugo pentaphylla Microtea debilis Fagopyrum tataricum

FIGURE S6. Maximum likelihood cladogram of Amaranthaceae s.l. inferred from IQ-tree

analysis of concatenated 76-plastid gene supermatrix. Numbers above branches indicate the

Quartet sampling internal node score. Quartet concordance/Quartet differential/ Quartet

informativeness. Scores in blue indicate strong support for the species tree topology, while red

scores indicate strong support for alternative topologies. a) BC1A ABC2 BC1C2 C1PA PAC2 3000 3000 3000 3000 2000 2000 2000 2000 2000

1000 1000 1000 1000 1000 Gene counts

0 0 0 0 0 H0 H1 H2 H0 H1 H2 H0 H1 H2 H0 H1 H2 H0 H1 H2

C1C2P C1C2A ABP C1BP PBC2 3000 3000 3000 3000 3000 2000 2000 2000 2000 2000

1000 1000 1000 1000

Gene counts 1000

0 0 0 0 0 H0 H1 H2 H0 H1 H2 H0 H1 H2 H0 H1 H2 H0 H1 H2

Raw BS ≥ 50

b) BC1A ABC2 BC1C2 C1PA PAC2 3000 3000 3000 3000 2000 2000 2000 2000 2000

1000 1000 1000 1000 1000 Gene counts

0 0 0 0 0 H0 H1 H2 H0 H1 H2 H0 H1 H2 H0 H1 H2 H0 H1 H2

C1C2P C1C2A ABP C1BP PBC2 3000 3000 3000 3000 3000 2000 2000 2000 2000 2000

1000 1000 1000 1000

Gene counts 1000

0 0 0 0 0 H0 H1 H2 H0 H1 H2 H0 H1 H2 H0 H1 H2 H0 H1 H2

Raw dAIC

FIGURE S7. Counts of gene tree inferences for the 10 quartets from the five main clades of

Amaranthaceae s.l. (a) Bars represent raw gene tree counts and counts of gene trees with

bootstrap support 50. Gene counts of constrained maximum likelihood searches for the 10

quartets from the five main clades of Amaranthaceae s.l. (b) Bars represent counts based on raw

maximum likelihood scores and counts based on trees with significant support (trees with a delta

corrected Akaike Information Criteria (ΔAICc) 2 than the next best model). H0 represents the

ASTRAL species tree of each quartet inferred. Each quartet is named following the species tree

topology, where the first two species are sister to each other (all topologies can be found in

Figure S6). A = Amaranthaceae. s.s. (Amaranthus hypochondriacus), B = Betoideae (Beta

vulgaris), C1 = Chenopods I (Chenopodium quinoa), C2 = Chenopods II (Caroxylum

vermiculatum), P = Polycnemoideae (Polycnemum majus).

FIGURE S8. Alignment and tree scores for each of the 10 quartets from the five main clades of Amaranthaceae s.l. Quartet Tree Certainty (TC) score distribution (a)

and its correlation with alignment length (b), alignment GC content (c), and alignment gap percentage (d). Quartets named following the ASTRAL species tree

topology (see Figure 6 for quartet topologies). A = Amaranthaceae. s.s. (Amaranthus hypochondriacus), B = Betoideae (Beta vulgaris), C1 = Chenopods I

(Chenopodium quinoa), C2 = Chenopods II (Caroxylum vermiculatum), P = Polycnemoideae (Polycnemum majus).

BC1A ABC2

Amaranthus_hyponchondriacus Amaranthus_hyponchondriacus Caroxylon_vermiculatum Amaranthus_hyponchondriacus 0.578 0.415 Chenopodium_quinoa Beta_vulgaris Amaranthus_hyponchondriacus Beta_vulgaris 0.422 Beta_vulgaris Chenopodium_quinoa Beta_vulgaris Caroxylon_vermiculatum 0.585 Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

Amaranthus_hyponchondriacus Chenopodium_quinoa Amaranthus_hyponchondriacus Amaranthus_hyponchondriacus 0.707 Beta_vulgaris Beta_vulgaris Caroxylon_vermiculatum Beta_vulgaris 0.46 0.293 Chenopodium_quinoa Amaranthus_hyponchondriacus Beta_vulgaris Caroxylon_vermiculatum 0.54 Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

Chenopodium_quinoa Amaranthus_hyponchondriacus Caroxylon_vermiculatum Caroxylon_vermiculatum 0.5 0.654 Beta_vulgaris Beta_vulgaris Amaranthus_hyponchondriacus Beta_vulgaris 0.5 0.346 Amaranthus_hyponchondriacus Chenopodium_quinoa Beta_vulgaris Amaranthus_hyponchondriacus Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

BC1C2 C1PA

Caroxylon_vermiculatum Beta_vulgaris Chenopodium_quinoa Amaranthus_hyponchondriacus 0.299 Chenopodium_quinoa Chenopodium_quinoa Amaranthus_hyponchondriacus Polycnemum_majus 0.252 Beta_vulgaris Caroxylon_vermiculatum Polycnemum_majus Chenopodium_quinoa 0.748 0.701 Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mecrygen_Mesembryanthemum_crystallinum

Caroxylon_vermiculatum Beta_vulgaris Chenopodium_quinoa Chenopodium_quinoa 0.317 0.749 Beta_vulgaris Chenopodium_quinoa Amaranthus_hyponchondriacus Polycnemum_majus 0.251 Chenopodium_quinoa Caroxylon_vermiculatum Polycnemum_majus Amaranthus_hyponchondriacus 0.683 Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mecrygen_Mesembryanthemum_crystallinum

Beta_vulgaris Caroxylon_vermiculatum Amaranthus_hyponchondriacus Amaranthus_hyponchondriacus 0.716 Chenopodium_quinoa Chenopodium_quinoa Chenopodium_quinoa Polycnemum_majus 0.298 0.284 Caroxylon_vermiculatum Beta_vulgaris Polycnemum_majus Chenopodium_quinoa 0.702 Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mecrygen_Mesembryanthemum_crystallinum

PAC2 C1C2P

0.81 0.883 Polycnemum_majus Amaranthus_hyponchondriacus Chenopodium_quinoa Caroxylon_vermiculatum 0.19 Caroxylon_vermiculatum Polycnemum_majus Caroxylon_vermiculatum Chenopodium_quinoa 0.117 Amaranthus_hyponchondriacus Caroxylon_vermiculatum Polycnemum_majus Polycnemum_majus

Mesembryanthemum_crystallinum Mecrygen_Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

Caroxylon_vermiculatum Caroxylon_vermiculatum Polycnemum_majus Caroxylon_vermiculatum 0.619 Amaranthus_hyponchondriacus Polycnemum_majus Chenopodium_quinoa Chenopodium_quinoa 0.381 0.42 Polycnemum_majus Amaranthus_hyponchondriacus Caroxylon_vermiculatum Polycnemum_majus 0.58 Mesembryanthemum_crystallinum Mecrygen_Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

Caroxylon_vermiculatum Amaranthus_hyponchondriacus Polycnemum_majus Polycnemum_majus 0.531 Polycnemum_majus Polycnemum_majus Caroxylon_vermiculatum Chenopodium_quinoa 0.421 0.469 Amaranthus_hyponchondriacus Caroxylon_vermiculatum Chenopodium_quinoa Caroxylon_vermiculatum 0.579 Mesembryanthemum_crystallinum Mecrygen_Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

C1C2A ABP

Amaranthus_hyponchondriacus Amaranthus_hyponchondriacus Polycnemum_majus Amaranthus_hyponchondriacus 0.629 Chenopodium_quinoa Chenopodium_quinoa Beta_vulgaris Beta_vulgaris 0.371 0.219 Caroxylon_vermiculatum Caroxylon_vermiculatum Amaranthus_hyponchondriacus Polycnemum_majus 0.781 Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

Caroxylon_vermiculatum Amaranthus_hyponchondriacus Amaranthus_hyponchondriacus Amaranthus_hyponchondriacus 0.827 Chenopodium_quinoa Chenopodium_quinoa Beta_vulgaris Beta_vulgaris 0.476 0.173 Amaranthus_hyponchondriacus Caroxylon_vermiculatum Polycnemum_majus Polycnemum_majus 0.524 Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

Amaranthus_hyponchondriacus Caroxylon_vermiculatum Polycnemum_majus Polycnemum_majus 0.557 Chenopodium_quinoa Chenopodium_quinoa Amaranthus_hyponchondriacus Beta_vulgaris 0.47 0.443 Caroxylon_vermiculatum Amaranthus_hyponchondriacus Beta_vulgaris Amaranthus_hyponchondriacus 0.53 Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

C1BP PBC2

Chenopodium_quinoa Chenopodium_quinoa Caroxylon_vermiculatum Caroxylon_vermiculatum 0.722 0.641 Polycnemum_majus Beta_vulgaris Beta_vulgaris Polycnemum_majus 0.278 0.359 Beta_vulgaris Polycnemum_majus Polycnemum_majus Beta_vulgaris

Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

Chenopodium_quinoa Chenopodium_quinoa Caroxylon_vermiculatum Beta_vulgaris 0.143 Beta_vulgaris Beta_vulgaris Polycnemum_majus Polycnemum_majus 0.857 0.362 Polycnemum_majus Polycnemum_majus Beta_vulgaris Caroxylon_vermiculatum 0.638 Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

Polycnemum_majus Polycnemum_majus Caroxylon_vermiculatum Caroxylon_vermiculatum 0.515 0.212 Chenopodium_quinoa Beta_vulgaris Beta_vulgaris Polycnemum_majus 0.485 Beta_vulgaris Chenopodium_quinoa Polycnemum_majus Beta_vulgaris 0.788 Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum Mesembryanthemum_crystallinum

FIGURE S9. Best three species networks for the 10 quartets from the five main clades of

Amaranthaceae s.l. Red and blue indicates the minor and major edges, respectively, of hybrid

nodes. Number next to the branches indicates inheritance probabilities for each hybrid node.

Network visualization with PhyloPlots (left) and network visualization with Dendroscope (right).

Each quartet is named following the species tree topology, where the first two are sisters (all topologies can be found in Figure S6). A = Amaranthaceae. s.s. (Amaranthus hypochondriacus),

B = Betoideae (Beta vulgaris), C1 = Chenopods I (Chenopodium quinoa), C2 = Chenopods II

(Caroxylum vermiculatum), P = Polycnemoideae (Polycnemum majus). H0 | | | | | | | | |

Chenopodium quinoa | | | | | | | | | | | | | | | |

Beta vulgaris | | | | | | | | | | | | | | | | |

Amaranthus hypocondriacus | | | | | | | | | | | |

Mesembryanthemum crystallinum | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |

H1 | Amaranthus hypocondriacus | | | | | Beta vulgaris | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Chenopodium quinoa | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |

Mesembryanthemum crystallinum | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | H2 | | | | | | | Amaranthus hypocondriacus | | | | | | | | | | | | | | | | | | | | | | | | | | | Chenopodium quinoa | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |

Beta vulgaris | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Mesembryanthemum crystallinum | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |

1 2 3 4 5 6 7 8 9

FIGURE S10 . Chromosomes of Beta vulgaris with gene tree topologies from the quartet BC1A

mapped. Each gene is colored according to gene tree topology (H0, H1, or H2). H0 represents

the ASTRAL species tree of the quartet. Longer colored lines along the chromosomes represent

syntenic genes (6,941) between Beta vulgaris and Mesembryanthemum crystallinum. Grey

represents genes not present in the ortholog set of the quartet BC1A. A = Amaranthaceae. s.s.

(Amaranthus hypochondriacus), B = Betoideae (Beta vulgaris), C1 = Chenopods I

(Chenopodium quinoa), C2 = Chenopods II (Caroxylum vermiculatum), P = Polycnemoideae

(Polycnemum majus). a) First and second codon postitions b) Only third codon position

● ● 0.11 0.35

● ● ● ● ● ●● ● ● ● 0.10 ● ● ● ●●● ● ●● ●●● ●● ●● ● ● ●

● 0.30 ●●● ● ● ● 0.09 ● ●●● ● ● ●● ● ● ● ● ●● ●● ●● ●● ●● ●● ● ●● ●● ●● ● ●●●

0.08 ● ● ●●● ● ● ●● ●● ● 0.25 ●● ●● ●● ● y = 0.8841002x 0.07

● ● Uncorrected genetic distance Uncorrected genetic distance

● = 0.06 y 0.5710071x

● 0.20

● ● 0.05

0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.20 0.25 0.30 0.35 0.40 0.45 0.50

Tr93 model distance Tr93 model distance

FIGURE S11. Saturation plots from the 11-taxon(tree) concatenated alignment. a) Saturation analysis for the first and second codon positions, and b) saturation analyses for the third codon position. Dotted lines represent expected unsaturated curves, and solid lines represent the observed saturation curves.

a) RSCU - Species

● Amaranthus_hyponchondriacus

● 0.02 Spinacia_oleracea

0.01 ● Chenopods II

● Chenopods I Achatocarpus_gracilis ● ● ● Betoideae Patellifolia_patellaris Chenopods I Caroxylon_vermiculatum ● Polycnemoideae ● ● Dim2 (14.4%) 0.00 Polycnemum_majus ● Amaranthaceae s.s.

● ● Outgroup Beta_vulgaris

−0.01

Hermbstaedtia_glau● ca

Chenopodium_quinoa● Tectico● rnia_pergranulata

● Nitrophila_occidentalis −0.05 0.00 0.05 Dim1 (71.2%)

b) RSCU - Codons CCG

GCG UCG

0.050 ACG

0.025 UUA CGA CUA UCC CCC AUC Dim2 (14.4%) GUA CAA ACC GAA AAC AAA UAC UUC UGU GGA CGG GCC G GGU AGA ACA AUA AC CAC CGU GU GUC CUC 0.000 GUU A CCA GGG CGC CAU CUU GAU UUG AAU UGC UU GCA GC UUU A GAG A GCU U U UCA A AAG GUG UCU CCU CAG GG GGC ACU A CUG −0.04 0.00 0.04 Dim1 (71.2%)

FIGURE S12. Correspondence analyses results of the Synonymous Codon Usage (RSCU) of the

11-taxon(tree) concatenated alignment. Results by a) species and (b) codons.

Tecticornia pergranulata a) Chenopods II b) Chenopods II Caroxylon vermiculatum Spinacia oleracea Chenopods I Chenopods I Chenopodium quinoa Beta vulgaris Betoideae Betoideae Patellifolia patellaris Polycnemum majus Polycnemoideae Polycnemoideae Nitrophila occidentalis Hermbstaedtia glauca Amaranthaceae Amaranthaceae Amaranthus hyponchondriacus s.s s.s Achatocarpus gracilis

c) Chenopods II d) Chenopods II

Chenopods I Chenopods I

Betoideae Betoideae

Polycnemoideae Polycnemoideae

Amaranthaceae Amaranthaceae s.s s.s

e) Chenopods II

Chenopods I a) – d) No paritition e) Codon partition Discordant 1 & 2 codon pos. (main alternative) All gene trees Betoideae Discordant (remaining Concordant Standard nucleotide alternatives) Genes with signal of coding compositional Polycnemoideae heterogeneity removed Degenarated coding Uninformative of 1 & 3 codon positions Amaranthaceae s.s

FIGURE S13. ASTRAL species trees from the 11-taxon(net) dataset estimated from gene trees inferred using multiple data schemes. a) Gene trees inferred with RAxML with a GTR-GAMMA model. b) Gene trees inferred with IQ-tree allowing for automatic model selection of sequence evolution. c) Gene trees inferred with RAxML with a GTR-GAMMA model and removal of genes that had signal of compositional heterogeneity. d) Gene trees inferred with IQ-tree allowing for automatic model selection of sequence evolution and removal of genes that had signal of compositional heterogeneity. a–d) Gene trees were inferred with no partition, codon partition (first and second codon, and third codon) and, only first and second codon positions

(third codon position removed and no partition). Gene trees were inferred using codon alignments with standard nucleotide coding, and alignments with degenerated coding of the first and third codon positions. e) All gene trees and gene trees after removal of genes that had signal of compositional heterogeneity, inferred with IQ-tree using amino acid sequences allowing for automatic model selection of sequence evolution. Pie charts on nodes present the proportion of gene trees that support that clade (blue), the proportion that support the main alternative bifurcation (green), the proportion that support the remaining alternatives (red), and the proportion (conflict or support) that have < 50% bootstrap support (gray).

Table S1. Taxon sampling and source of data No. of final CDS Reference coverage No. MO Perc. MO orthologs Family Subfamily Species code Genus Species Authority name Taxon name in tree and intermediate files Library reads single/paired-end Library stranded? used for BLASTN (Beta vulgaris ) orthologs (total 13024) Usage in previous phylotranscriptomic papers Source database Source accession Souce reference Souce title Amaranthaceae s.l. Betoideae Betamac Beta macrocarpa Guss. Betamac_Beta_macrocarpa Paired Non-stranded 17741 0.54 10279 78.9% --- SRA SRR1038481 Fan et al. 2015 Transcriptome Analysis of Beta macrocarpa and Identification of Differentially Expressed Transcripts in Response to Beet Necrotic Yellow Vein Virus Infection Amaranthaceae s.l. Betoideae FVXD Beta maritima L. FVXD_Beta_maritima Paired Non-stranded 15017 0.23 7774 59.7% used in Yang et. al 2015 SRA ERR2040223 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Amaranthaceae s.l. Betoideae Betatrig Beta vulgaris L. Betatrig_Beta_triginaᵃ Paired Stranded 17048 0.53 10662 81.9% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Amaranthaceae s.l. Betoideae Betavulgen Beta vulgaris L. Bevulgen_Beta_vulgaris ------26922 --- 11753 90.2% --- http://bvseq.molgen.mpg.de/index.shtml v.1.2 Dohm et al. 2013 The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) Amaranthaceae s.l. Betoideae Habtam Hablitzia tamnoides (C.A. Mey.) Bunge Habtam_Hablitzia_tamnoides Paired Stranded 15735 0.44 9809 75.3% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Amaranthaceae s.l. Betoideae Patpat Patellifolia patellaris (Moq.) A.J. Scott, Ford-Lloyd & J.T. Williams Patpat_Patellifolia_patellaris Paired Stranded 22777 0.53 11040 84.8% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Amaranthaceae s.l. Polycnemoideae MJM3242 Nitrophila occidentalis (Moq.) S. Watson MJM3242_Nitrophila_occidentalis Paired Stranded 39370 0.55 11649 89.4% used in Walker et al. 2018 SRA SRR6435357 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Amaranthaceae s.l. Polycnemoideae PolmaSFB Polycnemum majus A. Braun ex Bogenh. PolmaSFB_Polycnemum_majus Paired Stranded 42557 0.57 11668 89.6% used in Walker et al. 2018 SRA SRR6435356 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Amaranthaceae s.s. Achyranthoids Achbid Achyranthes bidentata Blume Achbid_Achyranthes_bidentata Paired Non-stranded 25583 0.5 8598 66.0% --- SRA SRR5591716 Yang et al. 2018 The root transcriptome of Achyranthes bidentata and the identification of the genes involved in the replanting benefit Amaranthaceae s.s. Achyranthoids NequaSFB Nelsia quadrangula Schinz NequaSFB_Nelsia_quadrangula Paired Stranded 24387 0.54 9313 71.5% used in Walker et al. 2018 SRA SRR6435358 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Amaranthaceae s.s. Aervoids HDSY Aerva javanica (Burm. f.) Juss. HDSY_Aerva_javanica Paired Non-stranded 27385 0.43 6929 53.2% used in Yang et. al 2015 SRA ERR2040202 /ERR2040203 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Amaranthaceae s.s. Aervoids PDQH Aerva lanata (L.) Juss. ex Schult. PDQH_Aerva_lanata Paired Non-stranded 19501 0.41 6879 52.8% used in Yang et. al 2015 SRA ERR2040200 /ERR2040201 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Amaranthaceae s.s. Aervoids MJM2678 Iresine arbuscula Uline & W.L. Bray MJM2678_Iresine_arbuscula Paired Stranded 26935 0.53 7997 61.4% used in Walker et al. 2018 SRA SRR6435327 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Amaranthaceae s.s. Aervoids MJM2943 Iresine rhizomatosa Standl. MJM2943_Iresine_rhizomatosa Paired Stranded 21890 0.53 7571 58.1% used in Walker et al. 2018 SRA SRR6435359 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Amaranthaceae s.s. Amaranthoids XSSD Amaranthus cruentus L. XSSD_Amaranthus_cruentus Paired Non-stranded 22359 0.48 10215 78.4% used in Yang et. al 2015 SRA ERR2040205 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Amaranthaceae s.s. Amaranthoids Amhy Amaranthus hypochondriacus L. Amhypgen_Amaranthus_hyponchondriacus ------23843 --- 10612 81.5% --- Phytozome v1.0 Lightfoot et al. 2017 Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution. Amaranthaceae s.s. Amaranthoids Ampal Amaranthus palmeri S. Watson Ampal_Amaranthus_palmeri Paired Non-stranded 23336 0.5 9960 76.5% --- SRA SRR5759382 Salas-Perez et al. 2018 RNA-Seq transcriptome analysis of Amaranthus palmeri with differential tolerance to glufosinate herbicide. Amaranthaceae s.s. Amaranthoids WMLW Amaranthus retroflexus L. WMLW_Amaranthus_retroflexus Paired Non-stranded 19417 0.29 7859 60.3% used in Yang et. al 2015 SRA ERR2040206 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Amaranthaceae s.s. Amaranthoids Amtric Amaranthus tricolor L. Amtric_Amaranthus_tricolor Paired Non-stranded 24201 0.5 9933 76.3% --- SRA SRR5930345 Liu et al. 2018 Identification of microRNAs in the green and red sectors of Amaranthus tricolor L. leaves based on Illumina sequencing data Amaranthaceae s.s. Amaranthoids Amtub Amaranthus tuberculatus (Moq.) J.D. Sauer Amtub_Amaranthus_tuberculatus Paired Non-stranded 22363 0.48 9965 76.5% --- SRA SRR6705609 --- Submitted to SRA in 2018. No reference found Amaranthaceae s.s. Celosioids Deeamar Deeringia amaranthoides (L.) Mears Deeamar_Deeringia_amaranthoides Paired Stranded 24155 0.52 10833 83.2% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Amaranthaceae s.s. Celosioids Hergla Hermbstaedtia glauca Reichb. ex Steud. Hergla_Hermbstaedtia_glauca Paired Stranded 24119 0.54 11212 86.1% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Amaranthaceae s.s. Gomphrenoids ZBPY Alternanthera brasiliana (L.) Kuntze ZBPY_Alternanthera_brasiliana Paired Non-stranded 39746 0.47 9141 70.2% used in Yang et. al 2015 SRA ERR2040215/ERR2040216 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Amaranthaceae s.s. Gomphrenoids OHKC Alternanthera caracasana Kunth OHKC_Alternanthera_caracasana Paired Non-stranded 41349 0.41 8905 68.4% used in Yang et. al 2015 SRA ERR2040217/ERR2040218 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Amaranthaceae s.s. Gomphrenoids Alph Alternanthera philoxeroides (Mart.) Griseb. Alph_Alternanthera_philoxeroides Paired Non-stranded 51167 0.52 9726 74.7% --- SRA SRR1661509 Liu et al. 2019 RNA sequencing characterizes transcriptome differences in cold response between northern and southern Alternanthera philoxeroides and highlight adaptations associated with northward expansion Amaranthaceae s.s. Gomphrenoids BWRK Alternanthera sessilis (L.) R. Br. ex DC. BWRK_Alternanthera_sessilis Paired Non-stranded 23148 0.42 8664 66.5% used in Yang et. al 2015 SRA ERR2040219 /ERR2040220 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Amaranthaceae s.s. Gomphrenoids EYRD Alternanthera tenella Colla EYRD_Alternanthera_tenella Paired Non-stranded 25884 0.4 8909 68.4% used in Yang et. al 2015 SRA ERR2040221/ERR2040222 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Amaranthaceae s.s. Gomphrenoids CUTE Blutaparon vermiculare (L.) Mears CUTE_Blutaparon_vermiculare Paired Non-stranded 18831 0.39 8661 66.5% used in Yang et. al 2015 SRA ERR2040207 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Amaranthaceae s.s. Gomphrenoids MJM1665 Froelichia latifolia R.A. McCauley MJM1665_Froelichia_latifolia Paired Stranded 30906 0.46 9395 72.1% used in Yang et. al 2018 SRA SRR1979685 Brockington et al 2015 Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales Amaranthaceae s.s. Gomphrenoids Gomcel Gomphrena celosoides Mart. Gomcel_Gomphrena_celosoides Paired Stranded 21652 0.5 10127 77.8% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Amaranthaceae s.s. Gomphrenoids Gomele Gomphrena elegans Mart. Gomele_Gomphrena_elegans Paired Stranded 26535 0.52 10147 77.9% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Amaranthaceae s.s. Gomphrenoids MJM1807 Gossypianthus lanuginosus (Poir.) Moq. MJM1807_Gossypianthus_lanuginosus Paired Stranded 19778 0.54 10319 79.2% used in Yang et. al 2018 SRA SRR6787476 Yang et al. 2018 Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events Amaranthaceae s.s. Gomphrenoids MJM2445 Guilleminea densa (Humb. & Bonpl. ex Schult.) Moq. MJM2445_Guilleminea_densa Paired Stranded 26558 0.53 10237 78.6% used in Yang et. al 2018 SRA SRR6787501 Yang et al. 2018 Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events Amaranthaceae s.s. Gomphrenoids Pfatub Pfaffia tuberosa (Spreng.) Hicken Pfatub_Pfaffia_tuberosa Paired Stranded 26649 0.5 9798 75.2% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Amaranthaceae s.s. Gomphrenoids Quaephe Quaternella ephedroides Pedersen Quaephe_Quaternella_ephedroides Paired Stranded 23950 0.47 9557 73.4% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Amaranthaceae s.s. Gomphrenoids MJM2259 Tidestromia lanuginosa (Nutt.) Standl. MJM2259_Tidestromia_lanuginosa Paired Stranded 24837 0.57 9779 75.1% used in Yang et. al 2018 SRA SRR6787504 Yang et al. 2018 Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events Amaranthaceae s.s. Gomphrenoids Tisp1013 Tidestromia oblongifolia (S. Watson) Standl. Tisp1013_Tidestromia_suffruticosaᵃ Paired Stranded 22679 0.51 9294 71.4% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Chenopodiaceae -- Bisi Bienertia sinuspersici Akhani Bisi_Bienertia_sinuspersici ------42004 0.43 9401 72.2% used in Yang et. al 2018 Not assembled. CDS from Yang et al. 2017 SRR1770364 Sharpe, 2014 Gene expression profiling in single cell c4 and related photosynthetic species in Suaedoideae Chenopodiaceae Camphorosmoideae WGET Bassia scoparia (L.) A.J. Scott WGET_Bassia_scoparia Paired Non-stranded 16019 0.3 8665 66.5% used in Yang et. al 2015 SRA ERR364385 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Chenopodiaceae Camphorosmoideae EosaxSFB Eokochia saxicola (Guss.) Freitag & G. Kadereit EosaxSFB_Eokochia_saxicola Paired Stranded 29936 0.55 11193 85.9% used in Walker et al. 2018 SRA SRR6435348 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Chenopodioideae ONLQ Atriplex hortensis L. ONLQ_Atriplex_hortensis Paired Non-stranded 19485 0.46 10536 80.9% used in Yang et. al 2015 SRA ERR2040208 /ERR2040209 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Chenopodiaceae Chenopodioideae Atrlen Atriplex lentiformis (Torr.) S. Watson Atrlen_Atriplex_lentiformis Paired Non-stranded 17454 0.5 10623 81.6% --- SRA SRR1041720 Li et al. 2015 Understanding the biochemical basis of temperature-induced lipid pathway adjustments in plants. Chenopodiaceae Chenopodioideae AAXJ Atriplex prostrata Boucher ex DC. AAXJ_Atriplex_prostrata Paired Non-stranded 19161 0.43 10285 79.0% used in Yang et. al 2015 SRA ERR2040210/ERR2040211 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Chenopodiaceae Chenopodioideae CBJR Atriplex rosea L. CBJR_Atriplex_rosea Paired Non-stranded 19991 0.45 10580 81.2% used in Yang et. al 2015 SRA ERR2040212/ERR2040213 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Chenopodiaceae Chenopodioideae MJM3295 Atriplex sp. MJM3295_Atriplex_sp Paired Stranded 20391 0.5 10901 83.7% used in Walker et al. 2018 SRA SRR6435344 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Chenopodioideae Chenbohen Blitum bonus-henricus (L.) C.A. Mey. Chenbohen_Chenopodium_bonus-henricus Paired Stranded 27367 0.54 11337 87.0% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Chenopodiaceae Chenopodioideae Cheama Chenopodium amaranticolor (H.J. Coste & A. Reyn.) H.J. Coste & A. Reyn. Cheama_Chenopodium_amaranticolor Paired Non-stranded 33616 0.44 9915 76.1% used in Yang et. al 2018 SRA SRR503600 Zhang et al. 2012 De novo foliar transcriptome of Chenopodium amaranticolor and analysis of its gene expression during virus-induced hypersensitive response Chenopodiaceae Chenopodioideae Chpal Chenopodium pallidicaule Aellen Chpal_Chenopodium_pallidicaule Paired Non-stranded 17132 0.51 3297 25.3% --- SRA SRR4425240 Jarvis et al. 2017 The genome of Chenopodium quinoa Chenopodiaceae Chenopodioideae Chquigen Chenopodium quinoa Willd. Chquigen_Chenopodium_quinoa ------44776 --- 11769 90.4% --- Phytozome v1.0 Jarvis et al. 2017 The genome of Chenopodium quinoa Chenopodiaceae Chenopodioideae Chsue Chenopodium suecicum J. Murr Chsue_Chenopodium_suecicum Paired Non-stranded 17928 0.5 9503 73.0% --- SRA SRR4425602 Jarvis et al. 2017 The genome of Chenopodium quinoa Chenopodiaceae Chenopodioideae Chenvul Chenopodium vulvaria L. Chenvul_Chenopodium_vulvaria Paired Stranded 16598 0.53 11153 85.6% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Chenopodiaceae Chenopodioideae Dysamb Dysphania ambrosioides (L.) Mosyakin & Clemants Dysamb_Dysphania_ambrosiaᵃ Paired Stranded 25436 0.54 11250 86.4% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Chenopodiaceae Chenopodioideae Dyapha Dysphania schraderiana (Schult.) Mosyakin & Clemants Dyapha_Dysphania_schraderiana Paired Non-stranded 14749 0.42 10070 77.3% --- SRA SRR5989515 --- Submitted to SRA in 2017. No refrence found Chenopodiaceae Chenopodioideae MJM3214 Extriplex californica (Moq.) E.H. Zacharias MJM3214_Extriplex_californica Paired Stranded 16229 0.51 10966 84.2% used in Yang et. al 2018 SRA SRR6787489 Yang et al. 2018 Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events Chenopodiaceae Chenopodioideae Grabra Grayia brandegeei A. Gray Grabra_Grayia_brandegeei Paired Stranded 15864 0.49 10554 81.0% used in Walker et al. 2018 SRA SRR6435284 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Chenopodioideae MJM3268 Grayia spinosa (Hook.) Moq. MJM3268_Grayia_spinosa Paired Stranded 16030 0.5 10664 81.9% used in Yang et. al 2018 SRA SRR6787510 Yang et al. 2018 Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events Chenopodiaceae Chenopodioideae MJM2311 Krascheninnikovia lanata (Pursh) A. Meeuse & A. Smit MJM2311_Krascheninnikovia_lanata Paired Stranded 18996 0.53 11264 86.5% used in Yang et. al 2018 SRA SRR6787516 Yang et al. 2018 Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events Chenopodiaceae Chenopodioideae Oxru Oxybasis rubra (L.) S. Fuentes-B., Uotila & Borsch Oxru_Oxybasis_rubra Paired Non-stranded 25776 0.53 11340 87.1% used in Walker et al. 2018 SRA SRR2913184 --- Submitted to SRA in 2015. No refrence found Chenopodiaceae Chenopodioideae MJM3031 Proatriplex pleiantha (W.A. Weber) Stutz & G.L. Chu MJM3031_Proatriplex_pleiantha Paired Stranded 14808 0.49 10299 79.1% used in Walker et al. 2018 SRA SRR6435312 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Chenopodioideae Spolegen Spinacia oleracea L. Spolegen_Spinacia_oleracea ------25495 --- 11586 89.0% --- Genome v1.0 Xu et al. 2017 Draft genome of spinach and transcriptome diversity of 120 Spinaciaaccessions Chenopodiaceae Chenopodioideae Spitet Spinacia tetrandra Steven ex M.Bieb. Spitet_Spinacia_tetrandra Single Non-stranded 18802 0.29 8819 67.7% used in Walker et al. 2018 SRA SRR1766331 Xu et al. 2017 Draft genome of spinach and transcriptome diversity of 120 Spinaciaaccessions Chenopodiaceae Chenopodioideae Spitur Spinacia turkestanica Iljin Spitur_Spinacia_turkestanica Single Non-stranded 9066 0.11 4256 32.7% Species used in Walker et al. 2018, but a different SRA accession SRA SRR1766333 Xu et al. 2017 Draft genome of spinach and transcriptome diversity of 120 Spinaciaaccessions Chenopodiaceae Chenopodioideae MJM3228 Stutzia covillei (Standl.) E.H. Zacharias MJM3228_Stutzia_covillei Paired Stranded 14806 0.39 9807 75.3% used in Walker et al. 2018 SRA SRR6435340 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Corispermoideae Agsq Agriophyllum squarrosum (L.) Moq. Agsq_Agriophyllum_squarrosum Paired Non-stranded 19671 0.54 11211 86.1% used in Yang et. al 2018 SRA SRR1559276 Zhao et al. 2014 Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation. Chenopodiaceae Corispermoideae MSB0000170SFB Corispermum hyssopifolium L. MSB0000170SFB_Corispermum_hyssopifolium Paired Stranded 16634 0.56 11409 87.6% used in Walker et al. 2018 SRA SRR6435347 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Salicornioideae SalspSFB Allenrolfea sp. SalspSFB_Allenrolfea_sp Paired Stranded 16123 0.51 10716 82.3% used in Walker et al. 2018 SRA SRR6435351 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Salicornioideae ArmacSFB Arthrocaulon macrostachyum (Moric.) Piirainen & G.Kadereit ArmacSFB_Arthrocnemum_macrostachyumᵃ Paired Stranded 18895 0.5 10634 81.6% used in Walker et al. 2018 SRA SRR6435310 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Salicornioideae Halcas Halostachys caspica C.A. Mey. ex Schrenk Halcas_Halostachys_caspica Paired Non-stranded 33573 0.49 10563 81.1% --- SRA SRR7003638 --- Submitted to SRA in 2018. No reference found Chenopodiaceae Salicornioideae Heteros Heterostachys sp. Heteros_Heterostachys_sp Paired Stranded 18385 0.47 10397 79.8% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Chenopodiaceae Salicornioideae KalcuSFB Kalidium cuspidatum (L.) Ung.-Sternb. KalcuSFB_Kalidium_cuspidatum Paired Stranded 18710 0.49 10190 78.2% used in Walker et al. 2018 SRA SRR6435350 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Salicornioideae Saeu2 Salicornia europaea L. Saeu2_Salicornia_europaea Paired Non-stranded 31052 0.37 9809 75.3% Species used in Walker et al. 2018, but a different SRA library SRA SRR823398 Ma et al. 2013 Global transcriptome profiling of Salicornia europaea L. shoots under NaCl treatment Chenopodiaceae Salicornioideae Salipac Salicornia pacifica Standl. Salipac_Salicornia_pacifica Paired Stranded 30611 0.53 10891 83.6% used in Walker et al. 2018 SRA SRR6435339 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Salicornioideae TecpeSFB Tecticornia pergranulata (L.) Dumort. TecpeSFB_Tecticornia_pergranulata Paired Stranded 26784 0.53 10898 83.7% used in Walker et al. 2018 SRA SRR6435313 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Salsoloidae AnaarSFB Anabasis articulata Moq. AnaarSFB_Anabasis_articulata Paired Stranded 21316 0.52 10112 77.6% used in Walker et al. 2018 SRA SRR6435311 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Salsoloidae CarveSFB Caroxylon vermiculatum (L.) Akhani & Roalson CarveSFB_Caroxylon_vermiculatum Paired Stranded 58480 0.55 11214 86.1% used in Walker et al. 2018 SRA SRR6435345 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Salsoloidae Hagl Halogeton glomeratus (M. Bieb.) C.A. Mey. Hagl_Halogeton_glomeratus Paired Non-stranded 24367 0.34 9248 71.0% used in Walker et al. 2018 SRA SRR1503502 Yao et al. 2018 Transcriptome sequencing and comparative analysis of differentially-expressed isoforms in the roots of Halogeton glomeratus under salt stress Chenopodiaceae Salsoloidae Haam Haloxylon ammodendron Bunge Haam_Haloxylon_ammodendron Paired Non-stranded 29314 0.55 10422 80.0% used in Yang et. al 2018 SRA SRR1697346 Long et al. 2014 De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. Chenopodiaceae Salsoloidae Hamsco Hammada scoparia Iljin Hamsco_Hammada_scoparia Single Non-stranded 23086 0.49 9787 75.1% --- SRA ERR2060287 Lauterbach et al. 2017 De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4Species of Tribe Salsoleae (Chenopodiaceae) Chenopodiaceae Salsoloidae MSB0496298SFB Kali collina Akhani & Roalson MSB0496298SFB_Kali_collina Paired Stranded 18660 0.55 10955 84.1% used in Walker et al. 2018 SRA SRR6435349 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Chenopodiaceae Salsoloidae Salopp Salsola oppositifolia Desf. Salopp_Salsola_oppositifolia Single Non-stranded 48370 0.49 10448 80.2% --- SRA ERR2060302 Lauterbach et al. 2017 De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4Species of Tribe Salsoleae (Chenopodiaceae) Chenopodiaceae Salsoloidae Salsod Salsola soda L. Salsod_Salsola_soda Single Non-stranded 18064 0.49 9714 74.6% --- SRA SRR3544552 Lauterbach et al. 2017 De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4Species of Tribe Salsoleae (Chenopodiaceae) Chenopodiaceae Salsoloidae Salweb Salsola webbii Moq. Salweb_Salsola_webbii Single Non-stranded 30337 0.49 10529 80.8% --- SRA ERR2060308 Lauterbach et al. 2017 De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4Species of Tribe Salsoleae (Chenopodiaceae) Chenopodiaceae Suaedoideae Suaara Suaeda aralocaspica Freitag & Schutze Suaara_Suaeda_aralocaspica Paired Non-stranded 18279 0.38 9879 75.9% --- SRA SRR3706496 Wang et al. 2017 Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination Chenopodiaceae Suaedoideae Suadivar Suaeda divaricata Moq. Suadivar_Suaeda_divaricata Paired Stranded 28206 0.5 10837 83.2% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Chenopodiaceae Suaedoideae Sufr Suaeda fruticosa Forssk. ex J.F. Gmel. Sufr_Suaeda_fruticosa Paired Non-stranded 12139 0.18 6473 49.7% used in Yang et. al 2018 SRA SRR1947661 Diray-Arce et al. 2015 ranscriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance Chenopodiaceae Suaedoideae Suagla Suaeda glauca (Bunge) Bunge Suagla_Suaeda_glauca Paired Non-stranded 16780 0.49 10454 80.3% --- SRA SRR2416214 Jin et al. 2016 Salt-Responsive Transcriptome Profiling of Suaeda glaucavia RNA Sequencing Chenopodiaceae Suaedoideae Suaifni Suaeda ifniensis Caball. ex Maire Suaifni_Suaeda_ifniensis Paired Stranded 17461 0.48 10477 80.4% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Chenopodiaceae Suaedoideae MJM1679 Suaeda linearis (Elliott) Moq. MJM1679_Suaeda_linearis Paired Stranded 33753 0.48 10648 81.8% used in Yang et. al 2018 SRA SRR6787513 Yang et al. 2017 Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events Chenopodiaceae Suaedoideae Suma Suaeda maritima (L.) Dumort. Suma_Suaeda_maritima Paired Non-stranded 46819 0.56 10828 83.1% used in Walker et al. 2018 SRA SRR3218589 Gharat et al. 2016 Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes Chenopodiaceae Suaedoideae Suasal Suaeda salsa Pall. Suasal_Suaeda_salsa Paired Non-stranded 18734 0.46 9991 76.7% --- SRA SRR5877201 Xu et al. 2017 Transcriptomic profiling of genes in matured dimorphic seeds of euhalophyte Suaeda salsa Chenopodiaceae Suaedoideae Suavera Suaeda vera Forssk. ex J.F. Gmel. Suavera_Suaeda_vera Paired Stranded 16827 0.48 10341 79.4% --- Newly sequenced Newly sequenced Newly sequenced Newly sequenced Chenopodiaceae Suaedoideae MJM3086 Suckleya suckleyana (Torr.) Rydb. MJM3086_Suckleya_suckleyana Paired Stranded 15189 0.51 10908 83.8% used in Walker et al. 2018 SRA SRR6435288 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Achatocarpaceae - OUTGROUP MJM2704 Achatocarpus gracilis H. Walter MJM2704_Achatocarpus_gracilis Paired Stranded 24544 0.48 10397 79.8% used in Walker et al. 2018 SRA SRR6435362 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Achatocarpaceae - OUTGROUP MJM1677 Phaulothamnus spinescens A. Gray MJM1677_Phaulothamnus_spinescens Paired Stranded 28006 0.45 9714 74.6% used in Yang et. al 2018 SRA SRR1979686 Brockington et al 2015 Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales Aizoaceae - OUTGROUP BJKT Delosperma echinatum (Lam.) Schwantes BJKT_Delosperma_echinatum Paired Non-stranded 18194 0.26 7498 57.6% used in Yang et. al 2018 SRA ERR2040192 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Aizoaceae - OUTGROUP Mecrygen Mesembryanthemum crystallinum L. Mecrygen_Mesembryanthemum_crystallinum ------25435 --- 10488 80.5% --- Yim and Cushman, Unpublished data ------Yim and Cushman, Unpublished data Caryophyllaceae - OUTGROUP CorSFB Corrigiola litoralis L. CorSFB_Corrigiola_litoralis Paired Stranded 19203 0.52 10577 81.2% used in Yang et. al 2018 SRA SRR6787499 Yang et al. 2018 Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. Caryophyllaceae - OUTGROUP Dicargen Dianthus caryophyllus L. Dicargen_Dianthus_caryophyllus ------43264 --- 7938 60.9% --- http://carnation.kazusa.or.jp DCA_r1.0 Yagi et al. 2014 Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). Caryophyllaceae - OUTGROUP HerSFB Herniaria latifolia Lapeyr. HerSFB_Herniaria_latifolia Paired Stranded 38364 0.54 9901 76.0% used in Yang et. al 2018 SRA SRR6787494 Yang et al. 2018 Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. Caryophyllaceae - OUTGROUP IlleSFB Illecebrum verticillatum L. IlleSFB_Illecebrum_verticillatum Paired Stranded 22434 0.5 9666 74.2% used in Yang et. al 2018 SRA SRR6787493 Yang et al. 2018 Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. Caryophyllaceae - OUTGROUP TJES Spergularia media (L.) C. Presl TJES_Spergularia_media Paired Non-stranded 21020 0.28 7643 58.7% used in Yang et. al 2015 SRA ERR2040231 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Microteaceae - OUTGROUP YNFJ Microtea debilis Sw. YNFJ_Microtea_debilis Paired Non-stranded 29481 0.34 8629 66.3% used in Yang et. al 2015 SRA ERR2040255 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Molluginaceae - OUTGROUP HURS Mollugo pentaphylla L. HURS_Mollugo_pentaphylla Paired Non-stranded 16900 0.36 7925 60.8% used in Yang et. al 2015 SRA ERR2040238 1KP/Matasci et al., 2014 Data access for the 1,000 Plants (1KP) project Nyctaginaceae - OUTGROUP MJM2726B Commicarpus scandens (L.) Standl. MJM2726B_Commicarpus_scandens Paired Stranded 24282 0.48 8747 67.2% used in Walker et al. 2018 SRA SRR6435360 Walker et al. 2018 From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales Polygonaceae - OUTGROUP Fatatgen Fagopyrum tataricum (L.) Gaertn. Fatatgen_Fagopyrum_tataricum ------31834 --- 6120 47.0% --- http://www.mbkbase.org/Pinku1 v2.0 Zhang et al. 2017 The Tartary Buckwheat Genome Provides Insights into Rutin Biosynthesis and Abiotic Stress Tolerance ᵃTaxon names updated in ms figures after analyses. Table S2. Voucher information of newly sequenced transcriptomes. Family Subfamily Species code Genus Species Authority name Voucher information Locality Growth condition Tissue RNA extraction RNA-seq library preparation Raw read pairs Filtered nuclear read pairs Filtered organelle read pairs Amaranthaceae s.l. Betoideae Betatrig Beta vulgaris L. Unvouchered Cultivated at Botanical Garden University Mainz, orig. coll. Bulgaria. Living Collection Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 22,125,749 12,050,145 9,280,410 Amaranthaceae s.l. Betoideae Habtam Hablitzia tamnoides (C.A. Mey.) Bunge Kadereit, G. s.n. (MJG 027642) Cultivated at Botanical Garden University Mainz, seeds obtained from a nursery Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 16,820,668 6,783,386 7,402,286 Amaranthaceae s.l. Betoideae Patpat Patellifolia patellaris (Moq.) A.J. Scott, Ford-Lloyd & J.T. Williams H. Freitag 40031 (MJG 013582) SW Morocco. Living Collection Botanic Garden Mainz 58. Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 20,112,651 12,691,402 6,396,902 Amaranthaceae s.s Celosioids Deeamar Deeringia amaranthoides (L.) Mears Millennium Seed Bank 301198 (MJG 023037) Orig. coll. China, Yunnan. Living Collection Botanic Garden Mainz 344. Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 21,713,722 17,238,976 3,048,492 Amaranthaceae s.s. Celosioids Hergla Hermbstaedtia glauca Reichb. ex Steud. Millennium Seed Bank 140498 (MJG 023036) Orig. coll. South Africa, Cape Provinces. Living Collection Botanic Garden Mainz 310. Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 21,285,421 16,726,894 3,619,788 Amaranthaceae s.s. Gomphrenoids Gomcel Gomphrena celosoides Mart. Aagesen, L. 41 (SI) Argentina, Misiones, Leandro N. Alem. Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 21,432,362 14,924,209 5,402,969 Amaranthaceae s.s. Gomphrenoids Gomele Gomphrena elegans Mart. R. Norte (MJG 027640) Argentina, Buenos Aires, Isidro; Cultivada en el vivero de Ribera norte. Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 21,301,322 14,457,205 5,711,422 Amaranthaceae s.s. Gomphrenoids Pfatub Pfaffia tuberosa (Spreng.) Hicken Aagesen, L. 51 (SI) Argentina, Corrientes, Santo Tomé. Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 21,358,353 11,557,356 8,516,444 Amaranthaceae s.s. Gomphrenoids Quaephe Quaternella ephedroides Pedersen Millennium Seed Bank 107437 (MJG 023038) Orig. coll. Brazil, Bahia Palmeiras. Living Collection Botanic Garden Mainz 270. Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 21,181,847 11,913,784 8,293,073 QIAGEN RNeasy Plant Mini Kit and QIAGEN RNAse-Free DNAse Set by Alfonso Timoneda at Brockington lab. KAPA Stranded RNA-Seq Library Preparation Kit (KK8420) with poly-A enrichment by Ning Wang at Smith Amaranthaceae s.s. Gomphrenoids Tisp1013 Tidestromia oblongifolia (S. Watson) Standl. CUBG 20160029 Cultivated at Rancho Santa Ana Botanical Garden Cultivated at Rancho Santa Ana Botanic Garden Leaf? Cambridge Sep 2016 Lab Oct 13, 2016 26,708,058 20,480,127 1,022,721 Chenopodiaceae Chenopodioideae Chenbohen Blitum bonus-henricus (L.) C.A Mey. Kadereit, G. s.n. (MJG 027643) Cultivated at Botanical Garden University Mainz. Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 20,383,537 13,403,745 5,683,389 Cultivated at Botanical Garden University of Mainz. Seeds obtained from Botanical Leaf, Chenopodiaceae Chenopodioideae Chenvul Chenopodium vulvaria L. Kadereit, G. s.n. (MJG 027658) Garden Innsbruck (Austria). Living Collection Botanic Garden Mainz 241. Cultivated at Botanical Garden University Mainz flower bud QIAGEN RNeasy Plant Mini Kit and QIAGEN RNAse-Free DNAse Set by Alfonso Timoneda at Brockington lab. TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 21,559,488 11,800,777 7,538,649 Chenopodiaceae Chenopodioideae Dysamb Dysphania ambrosioides (L.) Mosyakin & Clemants Millennium Seed Bank 57738 (MJG 022990) Cultivated at the Botanical Garden Mainz, orig. coll. unknown. Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 21,362,486 14,081,344 5,073,626 Cultivated at the Botanical Garden Mainz, orig. coll. San Antonio del Oeste, Rio Negro, Chenopodiaceae Salicornioideae Heteros Heterostachys olivascens Speg. Kadereit, G. s.n. (MJG 027635) Argentina, source seed exchange. Living Collection Botanic Garden Mainz 34. Cultivated at Botanical Garden University Mainz Leaf QIAGEN RNeasy Plant Mini Kit with in-column DNase digestion by Delphine Tefarikis at Kadereit Lab Jun 2018 TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 19,449,518 11,602,378 7,033,278 Leaf and Cultivated at the Botanical Garden Mainz, orig. coll. Comodoro Rivadavia, Chubut, apical Chenopodiaceae Suaedoideae Suadivar Suaeda divaricata Moq. Unvouchered Argentina; source seed exchange. Living Collection Botanic Garden Mainz 35. Cultivated at Botanical Garden University Mainz meristem QIAGEN RNeasy Plant Mini Kit and QIAGEN RNAse-Free DNAse Set by Alfonso Timoneda at Brockington lab. TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 20,571,773 15,310,442 4,298,598 Leaf and Cultivated at the Botanical Garden Mainz, orig. coll. SW Morocco, Merlift ca. 25 km apical Chenopodiaceae Suaedoideae Suaifni Suaeda ifniensis Caball. ex Maire H. Freitag 40022 (MJG 013577) behind NE Sidi Ifni. Living Collection Botanic Garden Mainz 205 (MJG 027655). Cultivated at Botanical Garden University Mainz meristem QIAGEN RNeasy Plant Mini Kit and QIAGEN RNAse-Free DNAse Set by Alfonso Timoneda at Brockington lab. TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 23,255,093 13,880,141 8,274,304 Leaf and Cultivated at Botanical Garden Mainz, seeds obtained from Botanical Garden Lisboa apical Chenopodiaceae Suaedoideae Suavera Suaeda vera Forssk. ex J.F. Gmel. Kadereit, G. s.n. (MJG 027641) (Portugal). Living Collection Botanic Garden Mainz 107. Cultivated at Botanical Garden University Mainz meristem QIAGEN RNeasy Plant Mini Kit and QIAGEN RNAse-Free DNAse Set by Alfonso Timoneda at Brockington lab. TruSeq Stranded Total RNA Library Prep Plant with RiboZero by U Minnesota Genomics Center Aug 2018 22,667,424 12,662,690 8,652,755 Table S3. Chloroplast references used for plastome assembly and tree inference. Family Genus Species Authority name Notes Source database Source code Souce reference Souce title Aizoaceae Mesembryanthemum crystallinum L. Used as reference and and tree inference - OUTGROUP GenBank NC_029049 --- Yim, Ha, and Cushman, 2016. Unpublished. Amaranthaceae Amaranthus hypochondriacus L. Used as reference and and tree inference GenBank NC_030770 Chaney et al. 2016 The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae) Betoideae Beta vulgaris L. Used as reference and and tree inference GenBank KR230391 Stadermann et al. 2015 SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris ) chloroplast genome Caryophyllaceae Dianthus caryophyllus L. Used as reference and and tree inference - OUTGROUP GenBank MG989277 Chen et al. 2018 Structural characteristic and phylogenetic analysis of the complete chloroplast genome of Dianthus caryophyllus . Chenopodiaceae Bienertia sinuspersici Akhani Used as reference and and tree inference GenBank KU726550 Kim et al. 2016 The complete chloroplast genome sequence of Bienertia sinuspersici Chenopodiaceae Chenopodium quinoa Willd. Used as reference and and tree inference GenBank NC_034949 Hong et al. 2017 Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album . Chenopodiaceae Haloxylon persicum Bunge ex Boiss. & Buhse Used only as assembly reference GenBank NC_027669 Dong et al. 2016 Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae) Chenopodiaceae Salicornia europaea L. Used only as assembly reference GenBank NC_027225 --- Ho et al., 2015. Unpublished. Chenopodiaceae Spinacia oleracea L. Used as reference and and tree inference GenBank NC_002202 Schmitz-Linneweber et al. 2001 The plastid chromosome of spinach (Spinacia oleracea ): complete nucleotide sequence and gene organization Chenopodiaceae Suaeda malacosperma Hara Used only as assembly reference GenBank MG813535 Park et al. 2018 The complete plastid genome of Suaeda malacosperma (Amaranthaceae/Chenopodiaceae), a vulnerable halophyte in coastal regions of Korea and Japan Montiaceae Cistanthe longiscapa (Barnéoud) Carolin ex Hershk. Used only as assembly reference GenBank NC_035140 Stroll et al. 2017 Development of microsatellite markers and assembly of the plastid genome in Cistanthe longiscapa (Montiaceae) based on low-coverage whole genome sequencing Polygonaceae Fagopyrum tataricum (L.) Gaertn. Used as reference and and tree inference - OUTGROUP GenBank NC_027161 Cho et al. 2015 Complete Chloroplast Genome Sequence of Tartary Buckwheat (Fagopyrum tataricum ) and Comparative Analysis with Common Buckwheat (F. esculentum ). Table S4. Assembled plastid CDS and alignment stats. Gene name No. taxa Alignment length No. nucleotides % missing data accD 74 1452 99245 7.6% atpA 100 1529 152424 0.3% atpB 93 1500 136630 2.1% atpE 81 408 32895 0.5% atpF 100 555 54953 1.0% atpH 100 246 24600 0.0% atpI 100 744 73977 0.6% ccsA 64 972 61080 1.8% cemA 93 690 63866 0.5% clpP 70 588 34555 16.0% infA 95 234 22196 0.2% matK 73 1588 102683 11.4% ndhA 92 1099 95991 5.1% ndhB 81 777 58130 7.6% ndhC 98 363 35574 0.0% ndhD 73 1505 103259 6.0% ndhE 62 306 18777 1.0% ndhF 51 2291 99017 15.3% ndhG 63 531 33326 0.4% ndhH 91 1182 106082 1.4% ndhI 76 513 38416 1.5% ndhJ 95 477 45315 0.0% ndhK 100 684 67804 0.9% petA 96 963 91872 0.6% petB 64 642 41072 0.0% petD 95 479 45372 0.3% petG 76 114 8664 0.0% petL 72 96 6896 0.2% petN 53 90 4770 0.0% psaA 101 2254 225017 1.2% psaB 100 2205 218615 0.9% psaC 59 246 14514 0.0% psaI 93 111 10323 0.0% psaJ 73 135 9844 0.1% psbA 80 1066 85280 0.0% psbB 100 1527 151853 0.6% psbC 103 1435 146143 1.1% psbD 101 1009 101607 0.3% psbE 94 252 23688 0.0% psbF 94 120 11280 0.0% psbH 77 222 17045 0.3% psbI 67 111 7417 0.3% psbJ 94 123 11562 0.0% Gene name No. taxa Alignment length No. nucleotides % missing data psbK 67 180 12058 0.0% psbL 94 117 10971 0.2% psbM 56 105 5880 0.0% psbN 76 132 10032 0.0% psbT 98 108 10497 0.8% psbZ 81 189 15309 0.0% rbcL 96 1428 134885 1.6% rpl2 85 825 70105 0.0% rpl14 95 366 34769 0.0% rpl16 92 358 32868 0.2% rpl20 85 387 32821 0.2% rpl22 88 599 50296 4.6% rpl23 82 268 21845 0.6% rpl32ᵃ 23 174 3956 1.1% rpl33 67 201 13402 0.5% rpl36 99 114 11257 0.3% rpoA 99 994 97641 0.8% rpoB 71 3261 176067 24.0% rpoC1 70 2049 129381 9.8% rpoC2 74 4267 235989 25.3% rps2 95 711 66704 1.2% rps3 92 657 59822 1.0% rps4 88 606 53206 0.2% rps7 90 468 42069 0.1% rps8 95 405 38475 0.0% rps11 98 417 40855 0.0% rps12 77 372 21630 24.5% rps14 96 303 28948 0.5% rps15 87 273 23680 0.3% rps16 64 268 16793 2.1% rps18 74 306 22618 0.1% rps19 86 279 23640 1.5% ycf2ᵃ 46 6514 258235 13.8% ycf3 93 515 43410 9.4% ycf4 96 555 52771 1.0% ᵃGene excluded from phylogenetic analyses due to low taxon occupancy Table S5. Model selection between maximum number of reticulations in species networks searches.

Maximum Number of number of Number Topology inferred ln(�) Parameters AICc �AICc BIC �BIC reticulations of loci reticulations allowed

Nuclear concatenated NA NA -24486.331 19 4138 49048.847 20589.6635 49130.8939 20546.6229 ASTRAL NA NA -23448.397 19 4138 46972.9794 18513.7959 47055.0262 18470.7552 cpDNA concatenated NA NA -24568.333 19 4138 49212.8503 20753.6668 49294.8971 20710.6261 Network 1 1 1 -21177.791 21 4138 42439.8068 13980.6233 42530.4696 13946.1986 Network 2 2 2 -17275.625 23 4138 34643.5188 6184.33532 34742.7937 6158.52273 Network 3 3 2 -16741.991 23 4138 33576.2506 5117.06715 33675.5256 5091.25455 Network 4 4 3 -15415.8 25 4138 30931.9164 2472.73289 31039.7994 2455.52844 Network 5 5 5 -14171.38 29 4138 28459.1835 0 28584.271 0 Table S6. Model selection between quartet tree topologies and species networks. Trees correspond to each of the three possible quartet topologies where H0 is the ASTRAL quartet species tree. Networks correspond to the best three networks for searches with one hybridization event allowed. Number of Quartetᵃ Topologyᵇ ln( ) Parameters AICc AICc BIC BIC � loci � � BC1A H0 -9014.809786 5 8258 18049.62684 24.73436754 18074.71426 14.70279692 H1 -9072.456373 5 8258 18164.92002 140.0275408 18190.00743 129.9959702 H2 -9073.888783 5 8258 18167.78484 142.8923611 18192.87225 132.8607905 Net 1 -8998.43945 7 8258 18024.89248 0 18060.01146 0 Net 2 -8998.439526 7 8258 18024.89263 0.000151947 18060.01162 0.000151947 Net 3 -8998.441478 7 8258 18024.89653 0.004056302 18060.01552 0.004056302 ABC2 H0 -8516.854413 5 7811 17053.71651 12.87079823 17078.52527 2.950887757 H1 -8581.563051 5 7811 17183.13379 142.2880731 17207.94254 132.3681626 H2 -8582.670875 5 7811 17185.34944 144.5037223 17210.15819 134.5838118 Net 1 -8506.415681 7 7811 17040.84572 0 17075.57438 0 Net 2 -8506.415769 7 7811 17040.84589 0.000176519 17075.57456 0.000176519 Net 3 -8506.42071 7 7811 17040.85577 0.010057548 17075.58444 0.010057548 BC1C2 H0 -9140.191425 5 8385 18300.39001 156.347016 18325.55385 146.2848258 H1 -9201.981045 5 8385 18423.96925 279.9262567 18449.13309 269.8640665 H2 -9214.405292 5 8385 18448.81775 304.7747517 18473.98158 294.7125615 Net 1 -9058.014812 7 8385 18144.04299 0 18179.26902 0 Net 2 -9058.019338 7 8385 18144.05205 0.009052497 18179.27807 0.009052497 Net 3 -9058.024046 7 8385 18144.06146 0.018468011 18179.28749 0.018468011 C1PA H0 -8932.927759 5 8134 17885.8629 0 17910.87456 0 H1 -8936.145955 5 8134 17892.29929 6.436391285 17917.31095 6.436391285 H2 -8936.481125 5 8134 17892.96963 7.106730999 17917.98129 7.106730999 Net 1 -8932.077808 7 8134 17892.1694 6.306498884 17927.18227 16.30771403 Net 2 -8932.078011 7 8134 17892.16981 6.306905172 17927.18268 16.30812032 Net 3 -8932.078714 7 8134 17892.17121 6.308310587 17927.18408 16.30952573 PAC2 H0 -8530.661274 5 7784 17081.33026 40.10000797 17106.12168 30.18704595 H1 -8552.9448 5 7784 17125.89731 84.66706025 17150.68873 74.75409823 H2 -8548.291438 5 7784 17116.59059 75.36033576 17141.382 65.44737374 Net 1 -8506.607925 7 7784 17041.23025 0 17075.93463 0 Net 2 -8506.609795 7 7784 17041.23399 0.00373969 17075.93837 0.00373969 Net 3 -8506.618966 7 7784 17041.25233 0.02208072 17075.95671 0.02208072 C1C2P H0 -9119.250871 5 8341 18258.50894 12.50997925 18283.64643 2.458344441 H1 -9163.685997 5 8341 18347.37919 101.38023 18372.51669 91.32859519 H2 -9164.83263 5 8341 18349.67246 103.6734974 18374.80995 93.62186263 Net 1 -9108.992761 7 8341 18245.99896 0 18281.18809 0 Net 2 -9108.994383 7 8341 18246.00221 0.003244509 18281.19133 0.003244509 Net 3 -9108.994843 7 8341 18246.00313 0.0041636 18281.19225 0.0041636 C1C2A H0 -8447.623029 5 7756 16915.2538 63.6063012 16940.02717 53.70057058 H1 -8520.509174 5 7756 17061.02609 209.378593 17085.79946 199.4728624 H2 -8522.764578 5 7756 17065.5369 213.889401 17090.31027 203.9836704 Net 1 -8411.816521 7 7756 16851.6475 0 16886.3266 0 Net 2 -8411.819912 7 7756 16851.65428 0.006781956 16886.33338 0.006781956 Net 3 -8411.820308 7 7756 16851.65507 0.007573446 16886.33417 0.007573446 ABP H0 -9008.115816 5 8206 18036.23895 3.307596079 18061.29474 -6.711300872 H1 -9015.941176 5 8206 18051.88967 18.95831519 18076.94546 8.939418238 H2 -9014.738462 5 8206 18049.48424 16.55288764 18074.54003 6.533990688 Net 1 -9002.458846 7 8206 18032.93135 0 18068.00604 0 Net 2 -9002.460142 7 8206 18032.93395 0.002592568 18068.00863 0.002592568 Net 3 -9002.464397 7 8206 18032.94246 0.011102577 18068.01714 0.011102577 C1BP H0 -9557.910518 5 8793 19135.82787 0 19161.22959 0 H1 -9661.475396 5 8793 19342.95762 207.1297559 19368.35935 207.1297559 H2 -9661.009687 5 8793 19342.0262 206.1983365 19367.42793 206.1983365 Net 1 -9556.24034 7 8793 19140.49343 4.665563813 19176.05266 14.82306554 Net 2 -9556.243036 7 8793 19140.49882 4.670955519 19176.05805 14.82845724 Net 3 -9556.246261 7 8793 19140.50527 4.677405326 19176.0645 14.83490705 PBC2 H0 -9158.309463 5 8379 18336.62609 0 18361.78635 0 H1 -9206.127177 5 8379 18432.26152 95.63542753 18457.42177 95.63542753 H2 -9205.933131 5 8379 18431.87343 95.24733612 18457.03368 95.24733612 Net 1 -9158.016519 7 8379 18344.04642 7.42032489 18379.26742 17.48107897 Net 2 -9158.017286 7 8379 18344.04795 7.421858749 18379.26896 17.48261282 Net 3 -9158.017377 7 8379 18344.04813 7.422042036 18379.26914 17.48279611 ᵃEach quartet is named following the species tree topology, where the first two are sister. A = Amaranthaceae. s.s. (Amaranthus hypochondriacus ), B = Betoideae (Beta vulgaris ), C1 = Chenopods I (Chenopodium quinoa ), C2 = Chenopods II (Caroxylum vermiculatum ), P = Polycnemoideae (Polycnemum majus ). ᵇAll quartet tree topologies can be found in Figure 5 and quartet network topologies in Figure S9. Table S7. Gene count based on raw likelihood, �AIC, and AU topology test. Trees correspond to each of the tree posible quartet topologiesᵃ where Raw bipartitions Bipartition with bootstrap >= 50 Raw likelihood �AIC AU topology test p-value Quartetᵇ Number of loci H0 H1 H2 H1 H2 H0 H0 H1 H2 H0 H1 H2 H0 H1 H2 Equivocal BC1A 8258 3218 2723 2317 2753 2243 1912 3268 2692 2298 2130 1636 1295 130 98 47 7017 ABC2 7811 3083 2521 2207 2666 2100 1804 3108 2502 2201 2085 1415 1252 204 68 47 6605 BC1C2 8385 3319 2988 2078 2819 2516 1682 3365 2969 2051 2228 1817 1133 204 127 49 6945 C1PA 8134 2819 2705 2610 2407 2241 2173 2850 2684 2600 1822 1619 1592 95 80 98 6925 PAC2 7784 2866 2216 2702 2444 1837 2286 2896 2210 2678 1876 1255 1605 120 67 96 6603 C1C2P 8341 3190 2738 2413 2741 2346 1982 3232 2720 2389 2091 1655 1378 173 97 88 6935 C1C2A 7756 3095 2619 2042 2679 2193 1670 3132 2588 2036 2054 1624 1136 153 107 53 6466 ABP 8206 2897 2532 2777 2444 2061 2320 2932 2526 2748 1859 1434 1583 134 56 52 6697 C1BP 8793 3573 2544 2676 3085 2070 2212 3609 2542 2642 2397 1433 1555 162 55 71 7429 PBC2 8379 3216 2554 2609 2764 2073 2160 3257 2527 2595 2136 1454 1523 165 68 90 7062

ᵃAll topologies can be found in Figure 5. ᵇEach quartet is named following the species tree topology, where the first two are sister. A = Amaranthaceae. s.s. (Amaranthus hypochondriacus ), B = Betoideae (Beta vulgaris ), C1 = Chenopods I (Chenopodium quinoa ), C2 = Chenopods II (Caroxylum vermiculatum ), P = Polycnemoideae (Polycnemum majus ). Table S8. Linear model results for correlation between quartet Tree consistency (TC) scores and alignment Alignment length Gap content GC content Quartetᵃ Sample size R2 p-value R2 p-value R2 p-value BC1A 8258 0.001147 0.002079 0.002228 1.78E-05 0.001008 0.003914 ABC2 7811 3.76E-05 0.5882 0.001275 0.001599 0.0006525 0.02397 BC1C2 8385 0.001113 0.002251 0.002348 9.02E-06 1.46E-04 0.2695 C1PA 8134 1.95E-04 0.2083 0.003885 1.85E-08 0.001725 0.0001788 PAC2 7784 2.06E-03 6.26E-05 0.008132 1.57E-15 0.001579 0.0004539 C1C2P 8341 0.002681 2.23E-06 0.005697 5.12E-12 0.0006883 0.01657 C1C2A 7756 0.0007874 1.35E-02 0.005023 4.14E-10 0.001103 0.003436 ABP 8206 0.0001394 0.2849 0.0008305 0.009037 0.0003169 0.1068 C1BP 8793 0.001477 0.0003123 0.003134 1.50E-07 0.001401 0.0004478 PBC2 8379 0.000225 0.1698 0.003343 1.18E-07 0.0005339 0.03442 ᵃEach quartet is named following the species tree topology, where the first two are sister. A = Amaranthaceae. s.s. (Amaranthus hypochondriacus ), B = Betoideae (Beta vulgaris ), C1 = Chenopods I (Chenopodium quinoa ), C2 = Chenopods II (Caroxylum vermiculatum ), P = Polycnemoideae (Polycnemum majus ).

Table S9. ABBA/BABA test results of Amaranthaceae s.l. five main groups quartets. Quartet (H0)a Number of loci Sites in alignment ABBA BABA Raw D-statistic Z-score P-value Introgression direction BC1Ab 8258 12778649 287226 254617 0.06018164 41.1085 ≤ 0.001 A⇔C1 ABC2 7811 12105324 252772 376755 -0.1969463 124.4161 ≤ 0.001 A⇔C2 BC1C2 8385 13192317 306570 258349 0.08535914 54.59751 ≤ 0.001 C1⇔C2 C1PAb 8134 12635201 342350 286813 0.08827124 64.62297 ≤ 0.001 A⇔P PAC2 7784 12049734 344726 405627 -0.08116313 42.88069 ≤ 0.001 C2⇔P C1C2Pb 8341 13127397 445384 276652 0.2336892 136.0151 ≤ 0.001 C2⇔P C1C2Ab 7756 12114778 396219 292561 0.1504951 101.3243 ≤ 0.001 A⇔C2 ABP 8206 12622625 276319 312060 -0.06074486 36.64264 ≤ 0.001 A⇔P C1BPb 8793 13712853 273286 261620 0.02180944 18.08364 ≤ 0.001 B⇔P PBC2 8379 13074019 217549 415616 -0.3128205 196.8972 ≤ 0.001 C2⇔P aEach quartet is named following the species tree topology, where the first two are sister. A = Amaranthaceae. s.s. (Amaranthus hypochondriacus ), B = Betoideae (Beta vulgaris ), C1 = Chenopods I (Chenopodium quinoa ), C2 = Chenopods II (Caroxylum vermiculatum ), P = Polycnemoideae (Polycnemum majus ). H0 topologies can be found in Figure 6 bQuartet compatible with the complete 105-taxon species trees Table S10. Anomaly zone limit calculations in 11-taxon species trees. Bold rows show pair of internodes in the anomaly zone when y < a(x). Species treea Clade (x)b Clade (y)b x y a(x) (C1, C2) (C1) 0.1467 2.722 0.1799 (C1, C2) (C2) 0.1467 2.1102 0.1799 ((C1, C2), B) (C1, C2) 0.1045 0.1467 0.3084 No partition ((C1, C2), B) (B) 0.1045 2.6081 0.3084 (((C1, C2), B), P) ((C1, C2), B) 0.0846 0.1045 0.4003 (((C1, C2), B), P) (P) 0.0846 3.5424 0.4003 aSpecies tree topology can be found in Figure 6. b B = Betoideae (Beta vulgaris ), C1 = Chenopods I (Chenopodium quinoa ), C2 = Chenopods II (Caroxylum vermiculatum ), P = Polycnemoideae (Polycnemum majus ).